5-2719242-T-C

Variant names:

• chr5-2719242-T-C
• rs2935598

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 0.714 in 152,112 control chromosomes in the GnomAD database, including 39,954 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 0.71 (39954 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 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: 0.714 AC: 108570 AN: 151996 Hom.: 39915 Cov.: 32

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.714 AC: 108659 AN: 152112 Hom.: 39954 Cov.: 32 AF XY: 0.711 AC XY: 52871 AN XY: 74348

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.715

Alfa AF: 0.665 Hom.: 5380

Bravo AF: 0.724

Asia WGS AF: 0.686 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2935598; hg19: chr5-2719356;