ENST00000837362.1:n.128-3180G>A

Variant names:

• chr12-121103909-C-T
• rs1796412
• ENST00000837362.1:n.128-3180G>A

Variant summary

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

The ENST00000837362.1(ENSG00000308932):​n.128-3180G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,150 control chromosomes in the GnomAD database, including 43,179 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 0.75 (43179 hom., cov: 35)
• Consequence: ENSG00000308932 ENST00000837362.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370031	XR_945457.2	n.2427+1005G>A		intron_variant	Intron 2 of 2
LOC105370031	XR_945458.2	n.1622+1005G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308932	ENST00000837362.1	n.128-3180G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113700 AN: 152032 Hom.: 43153 Cov.: 35

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.748 AC: 113774 AN: 152150 Hom.: 43179 Cov.: 35 AF XY: 0.751 AC XY: 55856 AN XY: 74384

African (AFR) AF: 0.631 AC: 26135 AN: 41432

American (AMR) AF: 0.830 AC: 12700 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2877 AN: 3472

East Asian (EAS) AF: 0.879 AC: 4566 AN: 5192

South Asian (SAS) AF: 0.737 AC: 3553 AN: 4824

European-Finnish (FIN) AF: 0.731 AC: 7743 AN: 10590

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53578 AN: 68018

Other (OTH) AF: 0.767 AC: 1623 AN: 2116

Alfa AF: 0.783 Hom.: 175601

Bravo AF: 0.753

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1796412; hg19: chr12-121541712;