rs7743338

Positions:

• chr6-80962233-G-A
• chr6-80962233-G-C
• chr6-80962233-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 0.494 in 151,480 control chromosomes in the GnomAD database, including 19,407 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 0.49 (19407 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 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: 0.493 AC: 74683 AN: 151362 Hom.: 19341 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.494 AC: 74802 AN: 151480 Hom.: 19407 Cov.: 31 AF XY: 0.499 AC XY: 36949 AN XY: 73978

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.485

Alfa AF: 0.436 Hom.: 1818

Bravo AF: 0.499

Asia WGS AF: 0.656 AC: 2274 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7743338; hg19: chr6-81671950;