rs2431337

chr5-103951778-C-T

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 0.88 in 152,242 control chromosomes in the GnomAD database, including 59,110 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 0.88 (59110 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.880 AC: 133837 AN: 152124 Hom.: 59075 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.879

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.880 AC: 133927 AN: 152242 Hom.: 59110 Cov.: 32 AF XY: 0.883 AC XY: 65720 AN XY: 74448

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.892

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.944

Gnomad4 NFE AF: 0.890

Gnomad4 OTH AF: 0.875

Alfa AF: 0.884 Hom.: 86371

Bravo AF: 0.872

Asia WGS AF: 0.958 AC: 3333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.70
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2431337; hg19: chr5-103287479; COSMIC: COSV60175895;