6-39733974-A-G

Variant names:

• chr6-39733974-A-G
• rs215497

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 0.568 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.758 AC: 31446 AN: 41490

American (AMR) AF: 0.557 AC: 8510 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1371 AN: 3464

East Asian (EAS) AF: 0.640 AC: 3304 AN: 5166

South Asian (SAS) AF: 0.606 AC: 2914 AN: 4810

European-Finnish (FIN) AF: 0.451 AC: 4765 AN: 10564

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.475 AC: 32293 AN: 67970

Other (OTH) AF: 0.556 AC: 1177 AN: 2116

Alfa AF: 0.534 Hom.: 7729

Bravo AF: 0.582

Asia WGS AF: 0.607 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.37
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs215497; hg19: chr6-39701750;