3-14638763-T-C

Variant names:

• chr3-14638763-T-C
• rs3846122
• ENST00000635800.1:n.319-1379T>C

Variant summary

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

The ENST00000635800.1(ENSG00000283392):​n.319-1379T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 152,052 control chromosomes in the GnomAD database, including 26,565 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 0.59 (26565 hom., cov: 32)
• Consequence: ENSG00000283392 ENST00000635800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

Genes affected

ENSG00000283392 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.644 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
ENSG00000283392	ENST00000635800.1	n.319-1379T>C		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89712 AN: 151934 Hom.: 26545 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.590 AC: 89778 AN: 152052 Hom.: 26565 Cov.: 32 AF XY: 0.590 AC XY: 43841 AN XY: 74324

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.585

Alfa AF: 0.603 Hom.: 3410

Bravo AF: 0.593

Asia WGS AF: 0.661 AC: 2300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3846122; hg19: chr3-14680270;