chr3-112368095-A-T

Variant names:

• chr3-112368095-A-T
• rs11708769
• ENST00000793787.1:n.423-1437T>A

Variant summary

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

The ENST00000793787.1(ENSG00000243081):​n.423-1437T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,082 control chromosomes in the GnomAD database, including 2,574 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 0.18 (2574 hom., cov: 32)
• Consequence: ENSG00000243081 ENST00000793787.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465
• Publications: 1 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 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.423-1437T>A		intron_variant	Intron 3 of 4
ENSG00000243081	ENST00000793789.1	n.312-1437T>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26678 AN: 151964 Hom.: 2567 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.176 AC: 26699 AN: 152082 Hom.: 2574 Cov.: 32 AF XY: 0.179 AC XY: 13313 AN XY: 74346

African (AFR) AF: 0.165 AC: 6855 AN: 41478

American (AMR) AF: 0.199 AC: 3041 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 589 AN: 3470

East Asian (EAS) AF: 0.431 AC: 2232 AN: 5174

South Asian (SAS) AF: 0.257 AC: 1239 AN: 4816

European-Finnish (FIN) AF: 0.162 AC: 1710 AN: 10580

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10363 AN: 67976

Other (OTH) AF: 0.176 AC: 370 AN: 2108

Alfa AF: 0.159 Hom.: 239

Bravo AF: 0.178

Asia WGS AF: 0.307 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.6
DANN	Benign	0.81
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs11708769; hg19: chr3-112086942;