rs7744020

Variant names:

• chr6-32658353-G-A
• rs7744020

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 0.335 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.335 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

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.366

Alfa AF: 0.324 Hom.: 2059

Bravo AF: 0.352

Asia WGS AF: 0.281 AC: 975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7744020; hg19: chr6-32626130;