4-103497082-G-T

Variant names:

• chr4-103497082-G-T
• rs340468
• ENST00000809036.1:n.116+2932G>T

Variant summary

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

The ENST00000809036.1(ENSG00000305137):​n.116+2932G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 151,886 control chromosomes in the GnomAD database, including 30,470 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 0.59 (30470 hom., cov: 31)
• Consequence: ENSG00000305137 ENST00000809036.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• Publications: 1 publications found

Genes affected

ENSG00000305137 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 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
ENSG00000305137	ENST00000809036.1	n.116+2932G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90146 AN: 151768 Hom.: 30455 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.594 AC: 90180 AN: 151886 Hom.: 30470 Cov.: 31 AF XY: 0.602 AC XY: 44657 AN XY: 74190

African (AFR) AF: 0.249 AC: 10293 AN: 41404

American (AMR) AF: 0.720 AC: 10990 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2422 AN: 3468

East Asian (EAS) AF: 0.922 AC: 4741 AN: 5140

South Asian (SAS) AF: 0.720 AC: 3468 AN: 4818

European-Finnish (FIN) AF: 0.712 AC: 7509 AN: 10546

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.716 AC: 48623 AN: 67938

Other (OTH) AF: 0.619 AC: 1301 AN: 2102

Alfa AF: 0.674 Hom.: 106517

Bravo AF: 0.580

Asia WGS AF: 0.760 AC: 2644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.57
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs340468; hg19: chr4-104418239;