chr3-118443544-T-C

Variant names:

• chr3-118443544-T-C
• rs10511379
• ENST00000482142.5:n.232+53079A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000482142.5(ENSG00000243276):​n.232+53079A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,290 control chromosomes in the GnomAD database, including 1,386 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 0.12 (1386 hom., cov: 33)
• Consequence: ENSG00000243276 ENST00000482142.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

Genes affected

ENSG00000243276 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.254 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
ENSG00000243276	ENST00000482142.5	n.232+53079A>G		intron_variant	Intron 3 of 6	5

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18852 AN: 152172 Hom.: 1379 Cov.: 33

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.0658

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.124 AC: 18858 AN: 152290 Hom.: 1386 Cov.: 33 AF XY: 0.126 AC XY: 9378 AN XY: 74466

Gnomad4 AFR AF: 0.0518

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.0663

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.108

Alfa AF: 0.137 Hom.: 732

Bravo AF: 0.124

Asia WGS AF: 0.129 AC: 451 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	2.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511379; hg19: chr3-118162391;