dbSNP rs1251078: ENSG00000297240:n.598C>G (chr1-75723803-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000746415.1(ENSG00000297240):n.598C>G 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 0.628 in 152,072 control chromosomes in the GnomAD database, including 30,090 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 0.63 ( 30088 hom., cov: 33)

Exomes 𝑓: 0.75 ( 2 hom. )

Consequence

ENSG00000297240
ENST00000746415.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.451

Publications

8 publications found

Variant links:

Genes affected

ENSG00000297240 (HGNC:):

ENSG00000297240 links:

SLC44A5 (HGNC:28524): (solute carrier family 44 member 5) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC44A5 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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC44A5	XM_017000610.2 link	c.-247+139G>C		intron_variant	Intron 1 of 25		XP_016856099.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000297240	ENST00000746415.1 link	n.598C>G	non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000293044	ENST00000433521.2 link	n.71-15G>C	intron_variant	Intron 1 of 3	3
ENSG00000293044	ENST00000648424.1 link	n.108+139G>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.628

AC:

95374

AN:

151944

Hom.:

30070

Cov.:

show subpopulations

Gnomad AFR

AF:

0.684

Gnomad AMI

AF:

0.637

Gnomad AMR

AF:

0.532

Gnomad ASJ

AF:

0.722

Gnomad EAS

AF:

0.713

Gnomad SAS

AF:

0.724

Gnomad FIN

AF:

0.614

Gnomad MID

AF:

0.669

Gnomad NFE

AF:

0.599

Gnomad OTH

AF:

0.628

GnomAD4 exome

AF:

0.750

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.833

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

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:

0.628

AC:

95439

AN:

152064

Hom.:

30088

Cov.:

AF XY:

0.629

AC XY:

46745

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.684

AC:

28358

AN:

41482

American (AMR)

AF:

0.531

AC:

8116

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.722

AC:

2503

AN:

3468

East Asian (EAS)

AF:

0.713

AC:

3688

AN:

5174

South Asian (SAS)

AF:

0.723

AC:

3488

AN:

4826

European-Finnish (FIN)

AF:

0.614

AC:

6478

AN:

10544

Middle Eastern (MID)

AF:

0.654

AC:

191

AN:

292

European-Non Finnish (NFE)

AF:

0.599

AC:

40709

AN:

67982

Other (OTH)

AF:

0.629

AC:

1327

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1847

3694

5540

7387

9234

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

792

1584

2376

3168

3960

<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:

0.609

Hom.:

3508

Bravo

AF:

0.621

Asia WGS

AF:

0.686

AC:

2385

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.27

(source)

DANN

Benign

0.53

PhyloP100

-0.45

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over