chr3-118106671-A-G

Variant names:

• chr3-118106671-A-G
• rs6794842
• ENST00000482142.5:n.233-19171T>C

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 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: ENSG00000243276 ENST00000482142.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48

Genes affected

ENSG00000243276 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243276	ENST00000482142.5	n.233-19171T>C		intron_variant	Intron 3 of 6	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;