chr6-150592825-T-A

Variant names:

• chr6-150592825-T-A
• rs9372078

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 0.732 in 152,064 control chromosomes in the GnomAD database, including 40,937 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 0.73 (40937 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111263 AN: 151944 Hom.: 40898 Cov.: 31

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.732 AC: 111362 AN: 152064 Hom.: 40937 Cov.: 31 AF XY: 0.734 AC XY: 54517 AN XY: 74316

African (AFR) AF: 0.769 AC: 31884 AN: 41470

American (AMR) AF: 0.686 AC: 10486 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2375 AN: 3462

East Asian (EAS) AF: 0.700 AC: 3619 AN: 5168

South Asian (SAS) AF: 0.727 AC: 3499 AN: 4810

European-Finnish (FIN) AF: 0.768 AC: 8106 AN: 10560

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48985 AN: 67996

Other (OTH) AF: 0.710 AC: 1495 AN: 2106

Alfa AF: 0.729 Hom.: 5026

Bravo AF: 0.729

Asia WGS AF: 0.708 AC: 2461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.79
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs9372078; hg19: chr6-150913961;