rs7744001

Variant names:

• chr6-32658309-G-A
• rs7744001

Your query was ambiguous. Multiple possible variants found:

• chr6-32658309-G-A
• chr6-32658309-G-C

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 0.35 in 151,542 control chromosomes in the GnomAD database, including 9,627 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 0.35 (9627 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 40 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.391 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: 0.350 AC: 52988 AN: 151424 Hom.: 9623 Cov.: 30

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.350 AC: 53012 AN: 151542 Hom.: 9627 Cov.: 30 AF XY: 0.348 AC XY: 25797 AN XY: 74074

African (AFR) AF: 0.396 AC: 16357 AN: 41282

American (AMR) AF: 0.378 AC: 5762 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1471 AN: 3470

East Asian (EAS) AF: 0.378 AC: 1943 AN: 5146

South Asian (SAS) AF: 0.405 AC: 1939 AN: 4782

European-Finnish (FIN) AF: 0.260 AC: 2731 AN: 10516

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21649 AN: 67814

Other (OTH) AF: 0.386 AC: 811 AN: 2100

Alfa AF: 0.323 Hom.: 23430

Bravo AF: 0.364

Asia WGS AF: 0.393 AC: 1364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.45
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs7744001; hg19: chr6-32626086;