6-43792190-G-A

Variant names:

• chr6-43792190-G-A
• rs7748962

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 0.848 in 152,220 control chromosomes in the GnomAD database, including 55,240 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 0.85 (55240 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.977 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: 0.848 AC: 129002 AN: 152102 Hom.: 55181 Cov.: 32

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.978

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.848 AC: 129120 AN: 152220 Hom.: 55240 Cov.: 32 AF XY: 0.854 AC XY: 63536 AN XY: 74424

African (AFR) AF: 0.940 AC: 39038 AN: 41542

American (AMR) AF: 0.877 AC: 13414 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2889 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5173 AN: 5174

South Asian (SAS) AF: 0.978 AC: 4724 AN: 4828

European-Finnish (FIN) AF: 0.809 AC: 8581 AN: 10604

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52551 AN: 67986

Other (OTH) AF: 0.835 AC: 1764 AN: 2112

Alfa AF: 0.800 Hom.: 27229

Bravo AF: 0.854

Asia WGS AF: 0.982 AC: 3413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.20
DANN	Benign	0.45
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7748962; hg19: chr6-43759927;