5-175439295-A-G

Variant names:

• chr5-175439295-A-G
• rs11749676

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 0.613 in 152,040 control chromosomes in the GnomAD database, including 29,043 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 0.61 (29043 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.84 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: 0.613 AC: 93191 AN: 151922 Hom.: 29032 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.613 AC: 93248 AN: 152040 Hom.: 29043 Cov.: 32 AF XY: 0.617 AC XY: 45874 AN XY: 74314

African (AFR) AF: 0.536 AC: 22213 AN: 41430

American (AMR) AF: 0.696 AC: 10644 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2376 AN: 3470

East Asian (EAS) AF: 0.861 AC: 4458 AN: 5176

South Asian (SAS) AF: 0.594 AC: 2868 AN: 4828

European-Finnish (FIN) AF: 0.624 AC: 6579 AN: 10550

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42049 AN: 67980

Other (OTH) AF: 0.649 AC: 1369 AN: 2110

Alfa AF: 0.270 Hom.: 3526

Bravo AF: 0.620

Asia WGS AF: 0.706 AC: 2454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.9
DANN	Benign	0.92
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs11749676; hg19: chr5-174866298; COSMIC: COSV67104355;