rs6586516

Variant names:

• chr1-17299036-T-C
• rs6586516

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 0.606 in 152,012 control chromosomes in the GnomAD database, including 28,590 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 0.61 (28590 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 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: 0.606 AC: 92019 AN: 151894 Hom.: 28536 Cov.: 31

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.606 AC: 92139 AN: 152012 Hom.: 28590 Cov.: 31 AF XY: 0.603 AC XY: 44791 AN XY: 74294

African (AFR) AF: 0.725 AC: 30052 AN: 41448

American (AMR) AF: 0.575 AC: 8776 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1621 AN: 3464

East Asian (EAS) AF: 0.367 AC: 1902 AN: 5182

South Asian (SAS) AF: 0.517 AC: 2485 AN: 4806

European-Finnish (FIN) AF: 0.566 AC: 5972 AN: 10560

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39286 AN: 67966

Other (OTH) AF: 0.606 AC: 1281 AN: 2114

Alfa AF: 0.593 Hom.: 9222

Bravo AF: 0.611

Asia WGS AF: 0.518 AC: 1804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.075
DANN	Benign	0.55
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs6586516; hg19: chr1-17625531;