rs1607979

Variant names:

• chr17-53255898-G-A
• rs1607979

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.313 in 151,752 control chromosomes in the GnomAD database, including 8,698 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 0.31 (8698 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47488 AN: 151636 Hom.: 8690 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.311

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.313 AC: 47498 AN: 151752 Hom.: 8698 Cov.: 31 AF XY: 0.324 AC XY: 23998 AN XY: 74120

African (AFR) AF: 0.164 AC: 6771 AN: 41410

American (AMR) AF: 0.423 AC: 6451 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1060 AN: 3468

East Asian (EAS) AF: 0.748 AC: 3841 AN: 5132

South Asian (SAS) AF: 0.496 AC: 2382 AN: 4804

European-Finnish (FIN) AF: 0.397 AC: 4164 AN: 10480

Middle Eastern (MID) AF: 0.302 AC: 87 AN: 288

European-Non Finnish (NFE) AF: 0.319 AC: 21681 AN: 67914

Other (OTH) AF: 0.319 AC: 671 AN: 2104

Alfa AF: 0.323 Hom.: 4235

Bravo AF: 0.313

Asia WGS AF: 0.603 AC: 2094 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.39
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1607979; hg19: chr17-51333259; COSMIC: COSV69487848;