rs4681346

Variant names:

• chr3-147098924-A-C
• rs4681346
• ENST00000473299.1:n.229+57541T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000473299.1(ENSG00000243620):​n.229+57541T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 152,100 control chromosomes in the GnomAD database, including 694 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 0.081 (694 hom., cov: 32)
• Consequence: ENSG00000243620 ENST00000473299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 3 publications found

Genes affected

ENSG00000243620 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 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
ENSG00000243620	ENST00000473299.1	n.229+57541T>G		intron_variant	Intron 3 of 5	4
ENSG00000243620	ENST00000670466.1	n.278-55593T>G		intron_variant	Intron 3 of 3
ENSG00000243620	ENST00000824672.1	n.98-55184T>G		intron_variant	Intron 1 of 2
ENSG00000243620	ENST00000824673.1	n.93-55187T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0810 AC: 12315 AN: 151982 Hom.: 695 Cov.: 32

Gnomad AFR AF: 0.0212

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.0862

Gnomad ASJ AF: 0.0889

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0447

Gnomad FIN AF: 0.0747

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0809 AC: 12312 AN: 152100 Hom.: 694 Cov.: 32 AF XY: 0.0773 AC XY: 5751 AN XY: 74356

African (AFR) AF: 0.0211 AC: 878 AN: 41546

American (AMR) AF: 0.0862 AC: 1314 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0889 AC: 308 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5146

South Asian (SAS) AF: 0.0444 AC: 214 AN: 4824

European-Finnish (FIN) AF: 0.0747 AC: 793 AN: 10620

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8331 AN: 67934

Other (OTH) AF: 0.0997 AC: 211 AN: 2116

Alfa AF: 0.103 Hom.: 108

Bravo AF: 0.0806

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.81
PhyloP100		0.18
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4681346; hg19: chr3-146816711;