rs7769979

Positions:

• chr6-32755795-G-A
• chr6-32755795-G-C
• chr6-32755795-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 0.5 in 151,428 control chromosomes in the GnomAD database, including 19,758 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 0.50 (19758 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75669 AN: 151310 Hom.: 19728 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.500 AC: 75759 AN: 151428 Hom.: 19758 Cov.: 32 AF XY: 0.510 AC XY: 37750 AN XY: 74006

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.530

Alfa AF: 0.466 Hom.: 7616

Bravo AF: 0.491

Asia WGS AF: 0.705 AC: 2446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7769979; hg19: chr6-32723572;