rs10511376

chr3-118447866-A-G

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, non coding transcript 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: ENST00000482142.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000482142.5	n.232+48757T>C		intron_variant, non_coding_transcript_variant		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;