rs3757388

Variant names:

• chr7-128935969-G-A
• rs3757388

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 0.548 in 151,874 control chromosomes in the GnomAD database, including 23,887 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 0.55 (23887 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.623 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: 0.549 AC: 83258 AN: 151756 Hom.: 23882 Cov.: 31

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.548 AC: 83292 AN: 151874 Hom.: 23887 Cov.: 31 AF XY: 0.547 AC XY: 40606 AN XY: 74184

African (AFR) AF: 0.404 AC: 16720 AN: 41404

American (AMR) AF: 0.515 AC: 7857 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2548 AN: 3470

East Asian (EAS) AF: 0.357 AC: 1846 AN: 5164

South Asian (SAS) AF: 0.609 AC: 2922 AN: 4800

European-Finnish (FIN) AF: 0.643 AC: 6766 AN: 10522

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42652 AN: 67942

Other (OTH) AF: 0.580 AC: 1226 AN: 2114

Alfa AF: 0.582 Hom.: 3311

Bravo AF: 0.530

Asia WGS AF: 0.469 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.59
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3757388; hg19: chr7-128576023;