rs246899

Variant names:

• chr5-103241438-T-A
• rs246899

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 0.315 in 151,770 control chromosomes in the GnomAD database, including 7,793 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 0.32 (7793 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 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: 0.315 AC: 47798 AN: 151652 Hom.: 7781 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.315 AC: 47837 AN: 151770 Hom.: 7793 Cov.: 31 AF XY: 0.309 AC XY: 22915 AN XY: 74166

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.292

Alfa AF: 0.319 Hom.: 988

Bravo AF: 0.317

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
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: rs246899; hg19: chr5-102577139; COSMIC: COSV72482521;