5-5510337-T-C

Variant names:

• chr5-5510337-T-C
• rs252929

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 0.608 in 152,090 control chromosomes in the GnomAD database, including 28,564 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 (28564 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 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: 0.608 AC: 92454 AN: 151972 Hom.: 28538 Cov.: 33

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.608 AC: 92526 AN: 152090 Hom.: 28564 Cov.: 33 AF XY: 0.604 AC XY: 44913 AN XY: 74368

African (AFR) AF: 0.545 AC: 22591 AN: 41460

American (AMR) AF: 0.654 AC: 9998 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2321 AN: 3468

East Asian (EAS) AF: 0.348 AC: 1802 AN: 5174

South Asian (SAS) AF: 0.641 AC: 3098 AN: 4830

European-Finnish (FIN) AF: 0.555 AC: 5871 AN: 10574

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44646 AN: 67980

Other (OTH) AF: 0.647 AC: 1366 AN: 2112

Alfa AF: 0.559 Hom.: 2605

Bravo AF: 0.614

Asia WGS AF: 0.528 AC: 1836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0020
DANN	Benign	0.22
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs252929; hg19: chr5-5510450; COSMIC: COSV53475545;