3-118443776-T-C

Variant names:

• chr3-118443776-T-C
• rs10511378
• ENST00000482142.5:n.232+52847A>G

Variant summary

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

The ENST00000482142.5(ENSG00000243276):​n.232+52847A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,218 control chromosomes in the GnomAD database, including 2,062 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 0.16 (2062 hom., cov: 33)
• Consequence: ENSG00000243276 ENST00000482142.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

Genes affected

ENSG00000243276 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 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+52847A>G		intron_variant	Intron 3 of 6	5

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24015 AN: 152100 Hom.: 2059 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0217

Gnomad SAS AF: 0.0935

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.158 AC: 24035 AN: 152218 Hom.: 2062 Cov.: 33 AF XY: 0.154 AC XY: 11475 AN XY: 74442

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.0216

Gnomad4 SAS AF: 0.0938

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.155

Alfa AF: 0.152 Hom.: 3908

Bravo AF: 0.159

Asia WGS AF: 0.0900 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511378; hg19: chr3-118162623;