rs10511379

Variant names:

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

Variant summary

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

The ENST00000833975.1(ENSG00000243276):​n.448+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 ENST00000833975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 3 publications found

Genes affected

ENSG00000243276 (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 (EAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000833975.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243276	ENST00000482142.5	TSL:5	n.232+53079A>G		intron	N/A
	ENSG00000243276	ENST00000833975.1		n.448+53079A>G		intron	N/A
	ENSG00000243276	ENST00000833976.1		n.349+53079A>G		intron	N/A

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

African (AFR) AF: 0.0518 AC: 2153 AN: 41570

American (AMR) AF: 0.155 AC: 2377 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 373 AN: 3472

East Asian (EAS) AF: 0.266 AC: 1373 AN: 5168

South Asian (SAS) AF: 0.0663 AC: 320 AN: 4830

European-Finnish (FIN) AF: 0.152 AC: 1611 AN: 10608

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10313 AN: 68026

Other (OTH) AF: 0.108 AC: 228 AN: 2116

Alfa AF: 0.137 Hom.: 822

Bravo AF: 0.124

Asia WGS AF: 0.129 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.74
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs10511379; hg19: chr3-118162391;