rs6693503

Variant names:

• chr1-19660801-A-G
• rs6693503

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 0.548 in 151,862 control chromosomes in the GnomAD database, including 23,878 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 0.55 (23878 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.505
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.638 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: 0.548 AC: 83159 AN: 151742 Hom.: 23876 Cov.: 30

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.548 AC: 83185 AN: 151862 Hom.: 23878 Cov.: 30 AF XY: 0.544 AC XY: 40343 AN XY: 74190

African (AFR) AF: 0.409 AC: 16931 AN: 41376

American (AMR) AF: 0.537 AC: 8206 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2071 AN: 3472

East Asian (EAS) AF: 0.185 AC: 953 AN: 5158

South Asian (SAS) AF: 0.509 AC: 2442 AN: 4802

European-Finnish (FIN) AF: 0.688 AC: 7242 AN: 10532

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43659 AN: 67936

Other (OTH) AF: 0.532 AC: 1122 AN: 2108

Alfa AF: 0.604 Hom.: 84450

Bravo AF: 0.532

Asia WGS AF: 0.365 AC: 1270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.9
DANN	Benign	0.56
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs6693503; hg19: chr1-19987294;