rs498843

Variant names:

• chr3-172014087-A-T
• rs498843

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 0.225 in 152,172 control chromosomes in the GnomAD database, including 4,324 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 0.22 (4324 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 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: 0.225 AC: 34151 AN: 152054 Hom.: 4318 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.0557

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.225 AC: 34179 AN: 152172 Hom.: 4324 Cov.: 32 AF XY: 0.217 AC XY: 16132 AN XY: 74400

African (AFR) AF: 0.324 AC: 13427 AN: 41492

American (AMR) AF: 0.177 AC: 2708 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3466

East Asian (EAS) AF: 0.0559 AC: 290 AN: 5190

South Asian (SAS) AF: 0.138 AC: 668 AN: 4824

European-Finnish (FIN) AF: 0.156 AC: 1648 AN: 10596

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13937 AN: 68002

Other (OTH) AF: 0.208 AC: 439 AN: 2114

Alfa AF: 0.228 Hom.: 540

Bravo AF: 0.228

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	10
DANN	Benign	0.72
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs498843; hg19: chr3-171731877;