chr5-103951778-C-T

Variant names:

• chr5-103951778-C-T
• rs2431337

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;