rs215497

Variant names:

• chr6-39733974-A-G
• rs215497

Your query was ambiguous. Multiple possible variants found:

• chr6-39733974-A-G
• chr6-39733974-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.568 in 152,062 control chromosomes in the GnomAD database, including 25,864 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 0.57 (25864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866

ACMG classification

Verdict is Benign. Variant got -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 = 0.751 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: 0.568 AC: 86262 AN: 151942 Hom.: 25831 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.568 AC: 86342 AN: 152062 Hom.: 25864 Cov.: 32 AF XY: 0.568 AC XY: 42237 AN XY: 74332

Gnomad4 AFR AF: 0.758

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.556

Alfa AF: 0.532 Hom.: 3997

Bravo AF: 0.582

Asia WGS AF: 0.607 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs215497; hg19: chr6-39701750;