5-175346986-A-G

Variant names:

• chr5-175346986-A-G
• rs2445803

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 0.735 in 152,048 control chromosomes in the GnomAD database, including 41,703 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 0.74 (41703 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• Publications: 4 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 = 0.823 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: 0.735 AC: 111710 AN: 151930 Hom.: 41655 Cov.: 31

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.735 AC: 111817 AN: 152048 Hom.: 41703 Cov.: 31 AF XY: 0.731 AC XY: 54304 AN XY: 74336

African (AFR) AF: 0.830 AC: 34441 AN: 41478

American (AMR) AF: 0.753 AC: 11517 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2453 AN: 3464

East Asian (EAS) AF: 0.364 AC: 1873 AN: 5144

South Asian (SAS) AF: 0.646 AC: 3110 AN: 4816

European-Finnish (FIN) AF: 0.681 AC: 7187 AN: 10560

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48940 AN: 67978

Other (OTH) AF: 0.737 AC: 1553 AN: 2108

Alfa AF: 0.721 Hom.: 138248

Bravo AF: 0.742

Asia WGS AF: 0.524 AC: 1822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.55
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2445803; hg19: chr5-174773989; COSMIC: COSV60236441;