rs7744001

chr6-32658309-G-Achr6-32658309-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.386

Alfa AF: 0.327 Hom.: 6574

Bravo AF: 0.364

Asia WGS AF: 0.393 AC: 1364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.3
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7744001; hg19: chr6-32626086;