7-132000775-C-T

Variant names:

• chr7-132000775-C-T
• rs10954350

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 0.866 in 152,158 control chromosomes in the GnomAD database, including 57,324 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 0.87 (57324 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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: 0.866 AC: 131703 AN: 152040 Hom.: 57266 Cov.: 31

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.866 AC: 131823 AN: 152158 Hom.: 57324 Cov.: 31 AF XY: 0.868 AC XY: 64518 AN XY: 74360

African (AFR) AF: 0.916 AC: 38025 AN: 41524

American (AMR) AF: 0.881 AC: 13464 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2756 AN: 3472

East Asian (EAS) AF: 0.985 AC: 5088 AN: 5164

South Asian (SAS) AF: 0.909 AC: 4373 AN: 4812

European-Finnish (FIN) AF: 0.847 AC: 8961 AN: 10582

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56437 AN: 68008

Other (OTH) AF: 0.852 AC: 1794 AN: 2106

Alfa AF: 0.842 Hom.: 79990

Bravo AF: 0.870

Asia WGS AF: 0.936 AC: 3256 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	0.033
DANN	Benign	0.68
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10954350; hg19: chr7-131685534;