7-128936032-T-C

Variant names:

• chr7-128936032-T-C
• rs3757387

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 0.377 in 151,898 control chromosomes in the GnomAD database, including 11,627 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 0.38 (11627 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 50 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 (NFE) allele frequency at 95% confidence interval = 0.442 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: 0.377 AC: 57274 AN: 151780 Hom.: 11629 Cov.: 31

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.377 AC: 57291 AN: 151898 Hom.: 11627 Cov.: 31 AF XY: 0.373 AC XY: 27673 AN XY: 74232

African (AFR) AF: 0.260 AC: 10766 AN: 41430

American (AMR) AF: 0.405 AC: 6176 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1812 AN: 3466

East Asian (EAS) AF: 0.122 AC: 630 AN: 5162

South Asian (SAS) AF: 0.397 AC: 1908 AN: 4804

European-Finnish (FIN) AF: 0.401 AC: 4230 AN: 10538

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30337 AN: 67940

Other (OTH) AF: 0.414 AC: 869 AN: 2098

Alfa AF: 0.408 Hom.: 1633

Bravo AF: 0.374

Asia WGS AF: 0.238 AC: 829 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	3.4
DANN	Benign	0.61
PhyloP100		-0.088

Splicing

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

Other links and lift over

dbSNP: rs3757387; hg19: chr7-128576086;