Genetic Variant RHCG:n.*523A>C (chr15-89471714-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000560081.5(RHCG):n.*523A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 152,756 control chromosomes in the GnomAD database, including 28,424 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.59 ( 28338 hom., cov: 32)

Exomes 𝑓: 0.53 ( 86 hom. )

Consequence

RHCG
ENST00000560081.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0880

Publications

7 publications found

Variant links:

Genes affected

RHCG (HGNC:18140): (Rh family C glycoprotein) Enables ammonium transmembrane transporter activity; ankyrin binding activity; and identical protein binding activity. Involved in ammonium transmembrane transport; cellular ion homeostasis; and transepithelial ammonium transport. Located in apical plasma membrane and basolateral plasma membrane. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

RHCG links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560081.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
RHCG	NM_016321.3	MANE Select	c.*166A>C	3_prime_UTR	Exon 11 of 11	NP_057405.1
RHCG	NR_110261.2		n.1558A>C	non_coding_transcript_exon	Exon 11 of 11
RHCG	NM_001321041.2		c.*155A>C	3_prime_UTR	Exon 11 of 11	NP_001307970.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
RHCG	ENST00000560081.5	TSL:1	n.*523A>C	non_coding_transcript_exon	Exon 11 of 11	ENSP00000453588.1
RHCG	ENST00000268122.9	TSL:1 MANE Select	c.*166A>C	3_prime_UTR	Exon 11 of 11	ENSP00000268122.4
RHCG	ENST00000560081.5	TSL:1	n.*523A>C	3_prime_UTR	Exon 11 of 11	ENSP00000453588.1

Frequencies

GnomAD3 genomes

AF:

0.595

AC:

90355

AN:

151950

Hom.:

28297

Cov.:

show subpopulations

Gnomad AFR

AF:

0.806

Gnomad AMI

AF:

0.696

Gnomad AMR

AF:

0.590

Gnomad ASJ

AF:

0.524

Gnomad EAS

AF:

0.377

Gnomad SAS

AF:

0.396

Gnomad FIN

AF:

0.490

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.517

Gnomad OTH

AF:

0.574

GnomAD4 exome

AF:

0.526

AC:

361

AN:

686

Hom.:

Cov.:

AF XY:

0.505

AC XY:

222

AN XY:

440

show subpopulations

African (AFR)

AF:

0.800

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.333

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.534

AC:

249

AN:

466

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.506

AC:

AN:

180

Other (OTH)

AF:

0.438

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.595

AC:

90450

AN:

152070

Hom.:

28338

Cov.:

AF XY:

0.589

AC XY:

43778

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.806

AC:

33452

AN:

41478

American (AMR)

AF:

0.590

AC:

9023

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.524

AC:

1818

AN:

3470

East Asian (EAS)

AF:

0.377

AC:

1943

AN:

5158

South Asian (SAS)

AF:

0.396

AC:

1913

AN:

4828

European-Finnish (FIN)

AF:

0.490

AC:

5174

AN:

10558

Middle Eastern (MID)

AF:

0.514

AC:

151

AN:

294

European-Non Finnish (NFE)

AF:

0.517

AC:

35131

AN:

67966

Other (OTH)

AF:

0.574

AC:

1212

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1812

3624

5436

7248

9060

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

724

1448

2172

2896

3620

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.535

Hom.:

24235

Bravo

AF:

0.614

Asia WGS

AF:

0.435

AC:

1512

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.6

(source)

DANN

Benign

0.79

PhyloP100

-0.088

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over