chr7-128267266-C-T

Variant names:

• chr7-128267266-C-T
• rs10954176

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.471 in 152,022 control chromosomes in the GnomAD database, including 18,024 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 0.47 (18024 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71586 AN: 151902 Hom.: 18031 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.471 AC: 71593 AN: 152022 Hom.: 18024 Cov.: 32 AF XY: 0.475 AC XY: 35262 AN XY: 74306

African (AFR) AF: 0.290 AC: 12045 AN: 41474

American (AMR) AF: 0.457 AC: 6993 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1788 AN: 3468

East Asian (EAS) AF: 0.827 AC: 4265 AN: 5156

South Asian (SAS) AF: 0.564 AC: 2719 AN: 4820

European-Finnish (FIN) AF: 0.538 AC: 5685 AN: 10558

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36446 AN: 67948

Other (OTH) AF: 0.489 AC: 1029 AN: 2106

Alfa AF: 0.504 Hom.: 30214

Bravo AF: 0.452

Asia WGS AF: 0.650 AC: 2260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	12
DANN	Benign	0.60
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10954176; hg19: chr7-127907319;