chr6-80962233-G-A

Variant names:

• chr6-80962233-G-A
• rs7743338

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.651 AC: 26950 AN: 41384

American (AMR) AF: 0.460 AC: 6967 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1361 AN: 3460

East Asian (EAS) AF: 0.684 AC: 3489 AN: 5098

South Asian (SAS) AF: 0.607 AC: 2929 AN: 4822

European-Finnish (FIN) AF: 0.444 AC: 4674 AN: 10530

Middle Eastern (MID) AF: 0.438 AC: 127 AN: 290

European-Non Finnish (NFE) AF: 0.397 AC: 26926 AN: 67742

Other (OTH) AF: 0.485 AC: 1018 AN: 2100

Alfa AF: 0.443 Hom.: 1972

Bravo AF: 0.499

Asia WGS AF: 0.656 AC: 2274 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.48
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs7743338; hg19: chr6-81671950;