rs10511379

Positions:

• chr3-118443544-T-C

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, non coding transcript 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: ENST00000482142.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000482142.5	n.232+53079A>G		intron_variant, non_coding_transcript_variant		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;