rs7744020

Variant names:

• chr6-32658353-G-A
• rs7744020

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 0.335 in 151,690 control chromosomes in the GnomAD database, including 8,852 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 0.33 (8852 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50775 AN: 151572 Hom.: 8849 Cov.: 30

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.335 AC: 50797 AN: 151690 Hom.: 8852 Cov.: 30 AF XY: 0.331 AC XY: 24496 AN XY: 74116

African (AFR) AF: 0.394 AC: 16284 AN: 41348

American (AMR) AF: 0.368 AC: 5622 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1310 AN: 3464

East Asian (EAS) AF: 0.246 AC: 1269 AN: 5152

South Asian (SAS) AF: 0.252 AC: 1208 AN: 4792

European-Finnish (FIN) AF: 0.259 AC: 2732 AN: 10542

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21265 AN: 67832

Other (OTH) AF: 0.366 AC: 767 AN: 2098

Alfa AF: 0.315 Hom.: 11688

Bravo AF: 0.352

Asia WGS AF: 0.281 AC: 975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.39
DANN	Benign	0.72
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs7744020; hg19: chr6-32626130;