rs12712936

Variant names:

• chr2-45163696-G-A
• rs12712936
• ENST00000716438.1:n.162-11444G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-45163696-G-A
• chr2-45163696-G-C
• chr2-45163696-G-T

Variant summary

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

The ENST00000716438.1(ENSG00000286728):​n.162-11444G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 152,052 control chromosomes in the GnomAD database, including 33,100 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 0.65 (33100 hom., cov: 32)
• Consequence: ENSG00000286728 ENST00000716438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296
• Publications: 1 publications found

Genes affected

ENSG00000286728 (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 (NFE) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716438.1. 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
	ENSG00000286728	ENST00000716438.1		n.162-11444G>A		intron	N/A
	ENSG00000286728	ENST00000716439.1		n.571-30128G>A		intron	N/A
	ENSG00000286728	ENST00000716440.1		n.137-30128G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99367 AN: 151934 Hom.: 33085 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.654 AC: 99417 AN: 152052 Hom.: 33100 Cov.: 32 AF XY: 0.652 AC XY: 48421 AN XY: 74320

African (AFR) AF: 0.523 AC: 21659 AN: 41444

American (AMR) AF: 0.647 AC: 9886 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2520 AN: 3466

East Asian (EAS) AF: 0.555 AC: 2868 AN: 5168

South Asian (SAS) AF: 0.594 AC: 2863 AN: 4816

European-Finnish (FIN) AF: 0.711 AC: 7528 AN: 10582

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.733 AC: 49861 AN: 67978

Other (OTH) AF: 0.668 AC: 1408 AN: 2108

Alfa AF: 0.691 Hom.: 54843

Bravo AF: 0.644

Asia WGS AF: 0.587 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.49
PhyloP100		0.30

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: rs12712936;

hg19: chr2-45390835;