rs1076151

Variant names:

• chr9-133633593-C-T
• rs1076151

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 0.29 in 151,968 control chromosomes in the GnomAD database, including 7,180 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 0.29 (7180 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.704 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: 0.290 AC: 44040 AN: 151850 Hom.: 7174 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.290 AC: 44080 AN: 151968 Hom.: 7180 Cov.: 32 AF XY: 0.302 AC XY: 22425 AN XY: 74282

African (AFR) AF: 0.309 AC: 12810 AN: 41440

American (AMR) AF: 0.320 AC: 4896 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1015 AN: 3468

East Asian (EAS) AF: 0.724 AC: 3715 AN: 5134

South Asian (SAS) AF: 0.506 AC: 2441 AN: 4820

European-Finnish (FIN) AF: 0.313 AC: 3304 AN: 10560

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14930 AN: 67936

Other (OTH) AF: 0.302 AC: 638 AN: 2112

Alfa AF: 0.236 Hom.: 864

Bravo AF: 0.292

Asia WGS AF: 0.604 AC: 2098 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	3.5
DANN	Benign	0.90
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs1076151; hg19: chr9-136498715;