rs1076150

Variant names:

• chr9-133633639-T-C
• rs1076150

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 0.455 in 151,990 control chromosomes in the GnomAD database, including 16,409 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 0.46 (16409 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 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: 0.455 AC: 69130 AN: 151872 Hom.: 16394 Cov.: 33

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.0845

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.455 AC: 69192 AN: 151990 Hom.: 16409 Cov.: 33 AF XY: 0.446 AC XY: 33154 AN XY: 74306

African (AFR) AF: 0.481 AC: 19957 AN: 41460

American (AMR) AF: 0.362 AC: 5531 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1470 AN: 3470

East Asian (EAS) AF: 0.0843 AC: 436 AN: 5170

South Asian (SAS) AF: 0.264 AC: 1272 AN: 4812

European-Finnish (FIN) AF: 0.455 AC: 4793 AN: 10536

Middle Eastern (MID) AF: 0.428 AC: 124 AN: 290

European-Non Finnish (NFE) AF: 0.506 AC: 34383 AN: 67938

Other (OTH) AF: 0.433 AC: 911 AN: 2106

Alfa AF: 0.481 Hom.: 33033

Bravo AF: 0.449

Asia WGS AF: 0.200 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.6
DANN	Benign	0.46
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1076150; hg19: chr9-136498761;