chr5-151094113-A-G

Variant names:

• chr5-151094113-A-G
• rs999556

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 0.389 in 152,104 control chromosomes in the GnomAD database, including 12,357 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 0.39 (12357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59052 AN: 151986 Hom.: 12313 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.389 AC: 59156 AN: 152104 Hom.: 12357 Cov.: 32 AF XY: 0.396 AC XY: 29481 AN XY: 74376

African (AFR) AF: 0.460 AC: 19095 AN: 41482

American (AMR) AF: 0.442 AC: 6753 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3466

East Asian (EAS) AF: 0.725 AC: 3742 AN: 5160

South Asian (SAS) AF: 0.562 AC: 2707 AN: 4818

European-Finnish (FIN) AF: 0.351 AC: 3711 AN: 10582

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20912 AN: 68004

Other (OTH) AF: 0.374 AC: 788 AN: 2108

Alfa AF: 0.344 Hom.: 31887

Bravo AF: 0.399

Asia WGS AF: 0.548 AC: 1903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.57
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs999556; hg19: chr5-150473674;