5-134904545-T-C

Variant names:

• chr5-134904545-T-C
• rs319598

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 0.632 in 151,818 control chromosomes in the GnomAD database, including 30,600 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 0.63 (30600 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 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: 0.632 AC: 95830 AN: 151700 Hom.: 30558 Cov.: 30

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.632 AC: 95920 AN: 151818 Hom.: 30600 Cov.: 30 AF XY: 0.634 AC XY: 47038 AN XY: 74170

African (AFR) AF: 0.736 AC: 30495 AN: 41436

American (AMR) AF: 0.620 AC: 9463 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2098 AN: 3468

East Asian (EAS) AF: 0.557 AC: 2847 AN: 5114

South Asian (SAS) AF: 0.542 AC: 2617 AN: 4830

European-Finnish (FIN) AF: 0.654 AC: 6892 AN: 10532

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39506 AN: 67878

Other (OTH) AF: 0.620 AC: 1304 AN: 2104

Alfa AF: 0.596 Hom.: 53883

Bravo AF: 0.631

Asia WGS AF: 0.552 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs319598; hg19: chr5-134240235; COSMIC: COSV54738862;