rs246899

Variant names:

• chr5-103241438-T-A
• rs246899

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 0.315 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.381 AC: 15748 AN: 41338

American (AMR) AF: 0.246 AC: 3751 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 777 AN: 3466

East Asian (EAS) AF: 0.317 AC: 1630 AN: 5144

South Asian (SAS) AF: 0.137 AC: 659 AN: 4818

European-Finnish (FIN) AF: 0.288 AC: 3040 AN: 10558

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21190 AN: 67910

Other (OTH) AF: 0.292 AC: 614 AN: 2106

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
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs246899; hg19: chr5-102577139; COSMIC: COSV72482521;