rs6861497

Variant names:

• chr5-102067882-A-G
• rs6861497

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 0.565 in 151,854 control chromosomes in the GnomAD database, including 24,323 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 0.56 (24323 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 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: 0.565 AC: 85665 AN: 151736 Hom.: 24297 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.565 AC: 85734 AN: 151854 Hom.: 24323 Cov.: 32 AF XY: 0.567 AC XY: 42077 AN XY: 74220

African (AFR) AF: 0.533 AC: 22102 AN: 41446

American (AMR) AF: 0.668 AC: 10177 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1623 AN: 3466

East Asian (EAS) AF: 0.703 AC: 3631 AN: 5162

South Asian (SAS) AF: 0.587 AC: 2826 AN: 4818

European-Finnish (FIN) AF: 0.561 AC: 5927 AN: 10562

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37609 AN: 67856

Other (OTH) AF: 0.582 AC: 1226 AN: 2106

Alfa AF: 0.560 Hom.: 52602

Bravo AF: 0.574

Asia WGS AF: 0.641 AC: 2222 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.55
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs6861497; hg19: chr5-101403586;