rs6457690

Variant names:

• chr6-32887940-G-A
• rs6457690

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 0.139 in 152,202 control chromosomes in the GnomAD database, including 1,753 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 0.14 (1753 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 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: 0.139 AC: 21131 AN: 152084 Hom.: 1748 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0884

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.139 AC: 21173 AN: 152202 Hom.: 1753 Cov.: 33 AF XY: 0.140 AC XY: 10401 AN XY: 74428

African (AFR) AF: 0.222 AC: 9229 AN: 41498

American (AMR) AF: 0.101 AC: 1538 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3470

East Asian (EAS) AF: 0.0884 AC: 459 AN: 5190

South Asian (SAS) AF: 0.154 AC: 746 AN: 4830

European-Finnish (FIN) AF: 0.114 AC: 1207 AN: 10594

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6972 AN: 68000

Other (OTH) AF: 0.129 AC: 272 AN: 2112

Alfa AF: 0.134 Hom.: 1036

Bravo AF: 0.138

Asia WGS AF: 0.146 AC: 507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.8
DANN	Benign	0.89
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs6457690; hg19: chr6-32855717;