ENST00000690965.1:n.440+13149G>A

Variant names:

• chr3-12218116-C-T
• rs310746
• ENST00000690965.1:n.440+13149G>A

Variant summary

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

The ENST00000690965.1(ENSG00000288952):​n.440+13149G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.936 in 152,016 control chromosomes in the GnomAD database, including 66,675 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 0.94 (66675 hom., cov: 32)
• Consequence: ENSG00000288952 ENST00000690965.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768

Genes affected

ENSG00000288952 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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
ENSG00000288952	ENST00000690965.1	n.440+13149G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.936 AC: 142125 AN: 151900 Hom.: 66616 Cov.: 32

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.936 AC: 142242 AN: 152016 Hom.: 66675 Cov.: 32 AF XY: 0.939 AC XY: 69787 AN XY: 74314

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.944

Gnomad4 ASJ AF: 0.946

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.965

Gnomad4 FIN AF: 0.941

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.941

Alfa AF: 0.912 Hom.: 82356

Bravo AF: 0.938

Asia WGS AF: 0.980 AC: 3408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs310746; hg19: chr3-12259616;