5-2719242-T-C

Variant names:

• chr5-2719242-T-C
• rs2935598

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 0.714 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.906 AC: 37619 AN: 41524

American (AMR) AF: 0.624 AC: 9535 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2438 AN: 3466

East Asian (EAS) AF: 0.515 AC: 2654 AN: 5158

South Asian (SAS) AF: 0.780 AC: 3759 AN: 4820

European-Finnish (FIN) AF: 0.625 AC: 6603 AN: 10568

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43743 AN: 67984

Other (OTH) AF: 0.715 AC: 1508 AN: 2110

Alfa AF: 0.673 Hom.: 11183

Bravo AF: 0.724

Asia WGS AF: 0.686 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.18
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs2935598; hg19: chr5-2719356;