rs3756311

chr5-150157517-A-G

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 0.483 in 152,050 control chromosomes in the GnomAD database, including 19,367 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 0.48 (19367 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 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: 0.482 AC: 73305 AN: 151932 Hom.: 19326 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.483 AC: 73411 AN: 152050 Hom.: 19367 Cov.: 32 AF XY: 0.480 AC XY: 35684 AN XY: 74338

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.493

Alfa AF: 0.452 Hom.: 1572

Bravo AF: 0.503

Asia WGS AF: 0.499 AC: 1735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.6
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3756311; hg19: chr5-149537080;