rs2914276

chr5-23542602-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0794

Gnomad4 ASJ AF: 0.0597

Gnomad4 EAS AF: 0.0478

Gnomad4 SAS AF: 0.0563

Gnomad4 FIN AF: 0.00791

Gnomad4 NFE AF: 0.0296

Gnomad4 OTH AF: 0.0758

Alfa AF: 0.0436 Hom.: 107

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2914276; hg19: chr5-23542711;