3-12218116-C-T

Variant names:

• chr3-12218116-C-T
• rs310746
• ENST00000690965.2:n.440+13149G>A

Variant summary

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

The ENST00000690965.2(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 ENST00000690965.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768
• Publications: 13 publications found

Genes affected

ENSG00000288952 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690965.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288952	ENST00000690965.2		n.440+13149G>A		intron	N/A
	ENSG00000288952	ENST00000764008.1		n.443+13149G>A		intron	N/A

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

African (AFR) AF: 0.975 AC: 40244 AN: 41288

American (AMR) AF: 0.944 AC: 14432 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.946 AC: 3285 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5187 AN: 5188

South Asian (SAS) AF: 0.965 AC: 4659 AN: 4826

European-Finnish (FIN) AF: 0.941 AC: 9986 AN: 10608

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61352 AN: 68026

Other (OTH) AF: 0.941 AC: 1986 AN: 2110

Alfa AF: 0.914 Hom.: 103784

Bravo AF: 0.938

Asia WGS AF: 0.980 AC: 3408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.7
DANN	Benign	0.61
PhyloP100		-0.77

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs310746;

hg19: chr3-12259616;