rs697763

Variant names:

• chr1-228004921-G-C
• rs697763

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 0.739 in 152,116 control chromosomes in the GnomAD database, including 42,383 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 0.74 (42383 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112273 AN: 151998 Hom.: 42326 Cov.: 32

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.739 AC: 112387 AN: 152116 Hom.: 42383 Cov.: 32 AF XY: 0.746 AC XY: 55493 AN XY: 74338

African (AFR) AF: 0.891 AC: 37001 AN: 41518

American (AMR) AF: 0.709 AC: 10839 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2279 AN: 3468

East Asian (EAS) AF: 0.900 AC: 4636 AN: 5150

South Asian (SAS) AF: 0.820 AC: 3948 AN: 4816

European-Finnish (FIN) AF: 0.741 AC: 7851 AN: 10590

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43495 AN: 67968

Other (OTH) AF: 0.717 AC: 1512 AN: 2110

Alfa AF: 0.698 Hom.: 4645

Bravo AF: 0.740

Asia WGS AF: 0.879 AC: 3057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.28
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs697763; hg19: chr1-228192622; COSMIC: COSV52729760;