chr5-150157517-A-G

Variant names:

• chr5-150157517-A-G
• rs3756311

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 0.483 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.702 AC: 29111 AN: 41462

American (AMR) AF: 0.451 AC: 6896 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1907 AN: 3470

East Asian (EAS) AF: 0.579 AC: 2983 AN: 5150

South Asian (SAS) AF: 0.424 AC: 2035 AN: 4802

European-Finnish (FIN) AF: 0.328 AC: 3467 AN: 10582

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25511 AN: 67982

Other (OTH) AF: 0.493 AC: 1039 AN: 2108

Alfa AF: 0.424 Hom.: 40056

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
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs3756311; hg19: chr5-149537080;