6-100473239-G-A

Variant names:

• chr6-100473239-G-A
• rs7773043

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 0.543 in 152,020 control chromosomes in the GnomAD database, including 22,569 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 0.54 (22569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.702 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: 0.543 AC: 82535 AN: 151902 Hom.: 22548 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.543 AC: 82590 AN: 152020 Hom.: 22569 Cov.: 32 AF XY: 0.545 AC XY: 40539 AN XY: 74318

African (AFR) AF: 0.540 AC: 22379 AN: 41438

American (AMR) AF: 0.501 AC: 7660 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1752 AN: 3470

East Asian (EAS) AF: 0.477 AC: 2461 AN: 5162

South Asian (SAS) AF: 0.722 AC: 3477 AN: 4818

European-Finnish (FIN) AF: 0.542 AC: 5732 AN: 10570

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37461 AN: 67968

Other (OTH) AF: 0.540 AC: 1139 AN: 2110

Alfa AF: 0.546 Hom.: 2806

Bravo AF: 0.532

Asia WGS AF: 0.594 AC: 2070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.1
DANN	Benign	0.58
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs7773043; hg19: chr6-100921115; COSMIC: COSV60255547;