rs10483374

Variant names:

• chr14-30356086-C-T
• rs10483374
• ENST00000820542.1:n.63-21269G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000820542.1(ENSG00000306731):​n.63-21269G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0146 in 152,262 control chromosomes in the GnomAD database, including 14 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 0.015 (14 hom., cov: 32)
• Consequence: ENSG00000306731 ENST00000820542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321
• Publications: 1 publications found

Genes affected

ENSG00000306731 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0146 (2225/152262) while in subpopulation AMR AF = 0.0191 (292/15288). AF 95% confidence interval is 0.0173. There are 14 homozygotes in GnomAd4. There are 1164 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 14 gene

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
ENSG00000306731	ENST00000820542.1	n.63-21269G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0146 AC: 2225 AN: 152144 Hom.: 14 Cov.: 32

Gnomad AFR AF: 0.00415

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0191

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0180

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0146 AC: 2225 AN: 152262 Hom.: 14 Cov.: 32 AF XY: 0.0156 AC XY: 1164 AN XY: 74462

African (AFR) AF: 0.00414 AC: 172 AN: 41552

American (AMR) AF: 0.0191 AC: 292 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0115 AC: 40 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5168

South Asian (SAS) AF: 0.00228 AC: 11 AN: 4830

European-Finnish (FIN) AF: 0.0404 AC: 429 AN: 10616

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0180 AC: 1222 AN: 68020

Other (OTH) AF: 0.0151 AC: 32 AN: 2114

Alfa AF: 0.0173 Hom.: 1

Bravo AF: 0.0124

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.72
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs10483374; hg19: chr14-30825292;