5-155414920-G-C

Variant names:

• chr5-155414920-G-C
• rs4958803

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 0.553 in 151,988 control chromosomes in the GnomAD database, including 24,593 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 (24593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83929 AN: 151870 Hom.: 24553 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.553 AC: 84022 AN: 151988 Hom.: 24593 Cov.: 32 AF XY: 0.553 AC XY: 41046 AN XY: 74274

African (AFR) AF: 0.744 AC: 30835 AN: 41452

American (AMR) AF: 0.616 AC: 9386 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1596 AN: 3466

East Asian (EAS) AF: 0.552 AC: 2844 AN: 5152

South Asian (SAS) AF: 0.566 AC: 2731 AN: 4822

European-Finnish (FIN) AF: 0.445 AC: 4706 AN: 10580

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30056 AN: 67952

Other (OTH) AF: 0.547 AC: 1155 AN: 2110

Alfa AF: 0.460 Hom.: 9296

Bravo AF: 0.575

Asia WGS AF: 0.579 AC: 2013 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs4958803; hg19: chr5-154794480; COSMIC: COSV65413690;