rs3757387

chr7-128936032-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.414

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3757387; hg19: chr7-128576086;