chr3-112371445-G-T

Variant names:

• chr3-112371445-G-T
• rs10934170
• ENST00000793787.1:n.423-4787C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000793787.1(ENSG00000243081):​n.423-4787C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,094 control chromosomes in the GnomAD database, including 2,433 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 0.17 (2433 hom., cov: 32)
• Consequence: ENSG00000243081 ENST00000793787.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717
• Publications: 6 publications found

Genes affected

ENSG00000243081 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 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
ENSG00000243081	ENST00000793787.1	n.423-4787C>A		intron_variant	Intron 3 of 4
ENSG00000243081	ENST00000793789.1	n.312-4787C>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25854 AN: 151976 Hom.: 2427 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.170 AC: 25878 AN: 152094 Hom.: 2433 Cov.: 32 AF XY: 0.174 AC XY: 12931 AN XY: 74372

African (AFR) AF: 0.164 AC: 6792 AN: 41486

American (AMR) AF: 0.193 AC: 2950 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 512 AN: 3472

East Asian (EAS) AF: 0.428 AC: 2214 AN: 5168

South Asian (SAS) AF: 0.237 AC: 1141 AN: 4822

European-Finnish (FIN) AF: 0.161 AC: 1705 AN: 10584

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.146 AC: 9915 AN: 67980

Other (OTH) AF: 0.170 AC: 358 AN: 2106

Alfa AF: 0.157 Hom.: 8742

Bravo AF: 0.173

Asia WGS AF: 0.298 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.47
DANN	Benign	0.37
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs10934170; hg19: chr3-112090292;