ENST00000837362.1:n.174+3064G>A

Variant names:

• chr12-121097619-C-T
• rs2516210
• ENST00000837362.1:n.174+3064G>A

Variant summary

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

The ENST00000837362.1(ENSG00000308932):​n.174+3064G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,048 control chromosomes in the GnomAD database, including 45,646 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 0.77 (45646 hom., cov: 31)
• Consequence: ENSG00000308932 ENST00000837362.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 3 publications found

Genes affected

ENSG00000308932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 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
ENSG00000308932	ENST00000837362.1	n.174+3064G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117462 AN: 151930 Hom.: 45621 Cov.: 31

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.773 AC: 117535 AN: 152048 Hom.: 45646 Cov.: 31 AF XY: 0.774 AC XY: 57507 AN XY: 74328

African (AFR) AF: 0.726 AC: 30066 AN: 41418

American (AMR) AF: 0.838 AC: 12804 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2877 AN: 3470

East Asian (EAS) AF: 0.880 AC: 4560 AN: 5182

South Asian (SAS) AF: 0.736 AC: 3549 AN: 4824

European-Finnish (FIN) AF: 0.722 AC: 7630 AN: 10572

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53388 AN: 67984

Other (OTH) AF: 0.786 AC: 1658 AN: 2110

Alfa AF: 0.779 Hom.: 23658

Bravo AF: 0.782

Asia WGS AF: 0.807 AC: 2805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.75
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2516210; hg19: chr12-121535422;