rs7752279

chr6-131791195-G-Achr6-131791195-G-T

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 0.593 in 152,066 control chromosomes in the GnomAD database, including 29,775 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 0.59 (29775 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 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: 0.592 AC: 89998 AN: 151948 Hom.: 29716 Cov.: 32

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.593 AC: 90120 AN: 152066 Hom.: 29775 Cov.: 32 AF XY: 0.595 AC XY: 44230 AN XY: 74312

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.587

Alfa AF: 0.520 Hom.: 2824

Bravo AF: 0.614

Asia WGS AF: 0.615 AC: 2140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.2
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7752279; hg19: chr6-132112335;