rs10511376

Variant names:

• chr3-118447866-A-G
• rs10511376
• ENST00000482142.5:n.232+48757T>C

Variant summary

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

The ENST00000482142.5(ENSG00000243276):​n.232+48757T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0388 in 152,266 control chromosomes in the GnomAD database, including 245 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 0.039 (245 hom., cov: 32)
• Consequence: ENSG00000243276 ENST00000482142.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17

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 (EAS) allele frequency at 95% confidence interval = 0.187 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+48757T>C		intron_variant	Intron 3 of 6	5

Frequencies

GnomAD3 genomes AF: 0.0387 AC: 5893 AN: 152148 Hom.: 244 Cov.: 32

Gnomad AFR AF: 0.0328

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0270

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0496

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0259

Gnomad OTH AF: 0.0364

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

GnomAD4 genome AF: 0.0388 AC: 5911 AN: 152266 Hom.: 245 Cov.: 32 AF XY: 0.0421 AC XY: 3131 AN XY: 74454

Gnomad4 AFR AF: 0.0331

Gnomad4 AMR AF: 0.0269

Gnomad4 ASJ AF: 0.0401

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0496

Gnomad4 NFE AF: 0.0259

Gnomad4 OTH AF: 0.0379

Alfa AF: 0.0373 Hom.: 17

Bravo AF: 0.0351

Asia WGS AF: 0.157 AC: 549 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511376; hg19: chr3-118166713;