17-63845125-G-C

Variant names:

• chr17-63845125-G-C
• rs2665797

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 0.695 in 152,008 control chromosomes in the GnomAD database, including 38,023 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 0.70 (38023 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 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: 0.695 AC: 105550 AN: 151890 Hom.: 37964 Cov.: 31

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.695 AC: 105665 AN: 152008 Hom.: 38023 Cov.: 31 AF XY: 0.695 AC XY: 51661 AN XY: 74296

African (AFR) AF: 0.900 AC: 37350 AN: 41490

American (AMR) AF: 0.632 AC: 9650 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1890 AN: 3472

East Asian (EAS) AF: 0.576 AC: 2971 AN: 5160

South Asian (SAS) AF: 0.748 AC: 3602 AN: 4816

European-Finnish (FIN) AF: 0.644 AC: 6801 AN: 10554

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.609 AC: 41390 AN: 67924

Other (OTH) AF: 0.654 AC: 1383 AN: 2114

Alfa AF: 0.523 Hom.: 1372

Bravo AF: 0.699

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.087
DANN	Benign	0.80
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2665797; hg19: chr17-61922485;