chr7-128932126-T-C

Variant names:

• chr7-128932126-T-C
• rs754281

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 0.753 in 151,458 control chromosomes in the GnomAD database, including 43,874 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 0.75 (43874 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.00
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.825 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: 0.753 AC: 113945 AN: 151340 Hom.: 43867 Cov.: 27

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.753 AC: 113992 AN: 151458 Hom.: 43874 Cov.: 27 AF XY: 0.752 AC XY: 55673 AN XY: 73998

African (AFR) AF: 0.624 AC: 25683 AN: 41188

American (AMR) AF: 0.662 AC: 10073 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3051 AN: 3468

East Asian (EAS) AF: 0.601 AC: 3076 AN: 5120

South Asian (SAS) AF: 0.831 AC: 3950 AN: 4756

European-Finnish (FIN) AF: 0.865 AC: 9123 AN: 10546

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.831 AC: 56376 AN: 67856

Other (OTH) AF: 0.754 AC: 1587 AN: 2104

Alfa AF: 0.770 Hom.: 7905

Bravo AF: 0.730

Asia WGS AF: 0.716 AC: 2489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.088
DANN	Benign	0.22
PhyloP100		-5.0

Splicing

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

Other links and lift over

dbSNP: rs754281; hg19: chr7-128572180;