rs3756311

Variant names:

• chr5-150157517-A-G
• rs3756311

Your query was ambiguous. Multiple possible variants found:

• chr5-150157517-A-G
• chr5-150157517-A-T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;