5-23542602-T-C

Variant names:

• chr5-23542602-T-C
• rs2914276

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 0.0727 in 152,264 control chromosomes in the GnomAD database, including 657 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 0.073 (657 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 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: 0.0725 AC: 11035 AN: 152146 Hom.: 655 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0795

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.0473

Gnomad SAS AF: 0.0561

Gnomad FIN AF: 0.00791

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0296

Gnomad OTH AF: 0.0757

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

GnomAD4 genome AF: 0.0727 AC: 11066 AN: 152264 Hom.: 657 Cov.: 31 AF XY: 0.0718 AC XY: 5343 AN XY: 74458

African (AFR) AF: 0.163 AC: 6771 AN: 41522

American (AMR) AF: 0.0794 AC: 1214 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0597 AC: 207 AN: 3470

East Asian (EAS) AF: 0.0478 AC: 247 AN: 5170

South Asian (SAS) AF: 0.0563 AC: 272 AN: 4830

European-Finnish (FIN) AF: 0.00791 AC: 84 AN: 10626

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0296 AC: 2014 AN: 68034

Other (OTH) AF: 0.0758 AC: 160 AN: 2110

Alfa AF: 0.0480 Hom.: 569

Bravo AF: 0.0817

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.38
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2914276; hg19: chr5-23542711;