7-127474085-C-T

Variant names:

• chr7-127474085-C-T
• rs10954158

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 0.328 in 152,040 control chromosomes in the GnomAD database, including 10,297 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 0.33 (10297 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 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: 0.328 AC: 49835 AN: 151922 Hom.: 10285 Cov.: 31

Gnomad AFR AF: 0.0912

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.328 AC: 49848 AN: 152040 Hom.: 10297 Cov.: 31 AF XY: 0.337 AC XY: 25018 AN XY: 74294

African (AFR) AF: 0.0910 AC: 3776 AN: 41496

American (AMR) AF: 0.376 AC: 5730 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 928 AN: 3468

East Asian (EAS) AF: 0.727 AC: 3765 AN: 5176

South Asian (SAS) AF: 0.419 AC: 2020 AN: 4826

European-Finnish (FIN) AF: 0.470 AC: 4957 AN: 10546

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27553 AN: 67960

Other (OTH) AF: 0.330 AC: 695 AN: 2108

Alfa AF: 0.361 Hom.: 1922

Bravo AF: 0.311

Asia WGS AF: 0.523 AC: 1813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.36
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10954158; hg19: chr7-127114139; COSMIC: COSV71521833;