chr7-128926978-T-C

Variant names:

• chr7-128926978-T-C
• rs4728141

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 0.392 in 151,868 control chromosomes in the GnomAD database, including 12,631 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 0.39 (12631 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.47 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: 0.392 AC: 59548 AN: 151750 Hom.: 12638 Cov.: 30

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.0788

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.392 AC: 59536 AN: 151868 Hom.: 12631 Cov.: 30 AF XY: 0.387 AC XY: 28694 AN XY: 74214

African (AFR) AF: 0.268 AC: 11104 AN: 41398

American (AMR) AF: 0.404 AC: 6160 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1778 AN: 3470

East Asian (EAS) AF: 0.0790 AC: 409 AN: 5178

South Asian (SAS) AF: 0.403 AC: 1938 AN: 4814

European-Finnish (FIN) AF: 0.422 AC: 4442 AN: 10514

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.474 AC: 32221 AN: 67936

Other (OTH) AF: 0.425 AC: 896 AN: 2108

Alfa AF: 0.436 Hom.: 1859

Bravo AF: 0.386

Asia WGS AF: 0.228 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4728141; hg19: chr7-128567032;