dbSNP rs6999: RTF2:n.2151A>G (chr20-56518845-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000477573.1(RTF2):n.2151A>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 0.412 in 151,908 control chromosomes in the GnomAD database, including 13,434 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 0.41 ( 13430 hom., cov: 31)

Exomes 𝑓: 0.53 ( 4 hom. )

Consequence

RTF2
ENST00000477573.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0160

Publications

14 publications found

Variant links:

Genes affected

RTF2 (HGNC:15890): (replication termination factor 2) Enables DNA binding activity. Involved in cellular response to hydroxyurea and regulation of DNA stability. Located in replication fork. [provided by Alliance of Genome Resources, Apr 2022]

RTF2 links:

GCNT7 (HGNC:16099): (glucosaminyl (N-acetyl) transferase family member 7) Predicted to enable acetylglucosaminyltransferase activity. Predicted to be involved in protein glycosylation. Predicted to be located in Golgi membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

GCNT7 links:

FAM209A (HGNC:16100): (family with sequence similarity 209 member A) Located in extracellular exosome and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

FAM209A 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 (NFE) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RTF2	NM_016407.5 link	c.*580A>G		3_prime_UTR_variant	Exon 9 of 9	ENST00000357348.10	NP_057491.2	Q9BY42

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RTF2	ENST00000357348.10 link	c.*580A>G		3_prime_UTR_variant	Exon 9 of 9	1	NM_016407.5	ENSP00000349906.6		Q9BY42
GCNT7	ENST00000243913.8 link	c.-929-4540T>C		intron_variant	Intron 1 of 6	2		ENSP00000243913.4		Q6ZNI0

Frequencies

GnomAD3 genomes

AF:

0.412

AC:

62503

AN:

151752

Hom.:

13426

Cov.:

show subpopulations

Gnomad AFR

AF:

0.431

Gnomad AMI

AF:

0.385

Gnomad AMR

AF:

0.363

Gnomad ASJ

AF:

0.310

Gnomad EAS

AF:

0.0567

Gnomad SAS

AF:

0.322

Gnomad FIN

AF:

0.444

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.447

Gnomad OTH

AF:

0.384

GnomAD4 exome

AF:

0.526

AC:

AN:

Hom.:

Cov.:

AF XY:

0.450

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

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:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.567

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

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:

0.412

AC:

62536

AN:

151870

Hom.:

13430

Cov.:

AF XY:

0.406

AC XY:

30113

AN XY:

74194

show subpopulations

African (AFR)

AF:

0.431

AC:

17852

AN:

41412

American (AMR)

AF:

0.362

AC:

5525

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.310

AC:

1075

AN:

3466

East Asian (EAS)

AF:

0.0566

AC:

292

AN:

5160

South Asian (SAS)

AF:

0.321

AC:

1547

AN:

4820

European-Finnish (FIN)

AF:

0.444

AC:

4663

AN:

10514

Middle Eastern (MID)

AF:

0.310

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.447

AC:

30333

AN:

67928

Other (OTH)

AF:

0.383

AC:

807

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1782

3564

5345

7127

8909

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

584

1168

1752

2336

2920

<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:

0.428

Hom.:

12642

Bravo

AF:

0.403

Asia WGS

AF:

0.197

AC:

688

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

1.2

(source)

DANN

Benign

0.55

PhyloP100

0.016

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over