rs6457938

Variant names:

• chr6-36692676-A-G
• rs6457938

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 0.636 in 152,022 control chromosomes in the GnomAD database, including 31,162 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 0.64 (31162 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.630
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 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: 0.636 AC: 96606 AN: 151904 Hom.: 31116 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.636 AC: 96705 AN: 152022 Hom.: 31162 Cov.: 32 AF XY: 0.637 AC XY: 47365 AN XY: 74324

African (AFR) AF: 0.735 AC: 30460 AN: 41452

American (AMR) AF: 0.581 AC: 8883 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2301 AN: 3470

East Asian (EAS) AF: 0.682 AC: 3524 AN: 5168

South Asian (SAS) AF: 0.671 AC: 3237 AN: 4824

European-Finnish (FIN) AF: 0.586 AC: 6179 AN: 10548

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39966 AN: 67964

Other (OTH) AF: 0.648 AC: 1368 AN: 2112

Alfa AF: 0.607 Hom.: 45763

Bravo AF: 0.635

Asia WGS AF: 0.695 AC: 2417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.55
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs6457938; hg19: chr6-36660453;