chr3-118106671-A-G

Position:

• chr3-118106671-A-G

Variant summary

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

The ENST00000482142.5(ENSG00000243276):​n.233-19171T>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 0.376 in 151,910 control chromosomes in the GnomAD database, including 11,319 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 0.38 (11319 hom., cov: 32)
• Consequence: ENST00000482142.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 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.233-19171T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57065 AN: 151792 Hom.: 11281 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.376 AC: 57164 AN: 151910 Hom.: 11319 Cov.: 32 AF XY: 0.375 AC XY: 27854 AN XY: 74238

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.387

Alfa AF: 0.355 Hom.: 1710

Bravo AF: 0.395

Asia WGS AF: 0.474 AC: 1650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6794842; hg19: chr3-117825518;