rs149392

Variant names:

• chr6-32922194-T-C
• rs149392

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 0.0875 in 152,218 control chromosomes in the GnomAD database, including 635 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 0.088 (635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.126 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: 0.0874 AC: 13287 AN: 152102 Hom.: 629 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0505

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.0857

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.0806

Gnomad OTH AF: 0.0727

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

GnomAD4 genome AF: 0.0875 AC: 13322 AN: 152218 Hom.: 635 Cov.: 32 AF XY: 0.0902 AC XY: 6713 AN XY: 74414

African (AFR) AF: 0.102 AC: 4248 AN: 41530

American (AMR) AF: 0.0505 AC: 772 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0588 AC: 204 AN: 3472

East Asian (EAS) AF: 0.0857 AC: 444 AN: 5182

South Asian (SAS) AF: 0.134 AC: 648 AN: 4826

European-Finnish (FIN) AF: 0.112 AC: 1192 AN: 10600

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.0806 AC: 5484 AN: 67998

Other (OTH) AF: 0.0753 AC: 159 AN: 2112

Alfa AF: 0.0835 Hom.: 878

Bravo AF: 0.0809

Asia WGS AF: 0.132 AC: 455 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.76
PhyloP100		-0.022

Splicing

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

Other links and lift over

dbSNP: rs149392; hg19: chr6-32889971;