rs12712001

Variant names:

• chr2-4373268-G-A
• rs12712001
• ENST00000707165.1:n.260-65698G>A

Variant summary

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

The ENST00000707165.1(ENSG00000291325):​n.260-65698G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0889 in 152,220 control chromosomes in the GnomAD database, including 1,012 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 0.089 (1012 hom., cov: 33)
• Consequence: ENSG00000291325 ENST00000707165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 1 publications found

Genes affected

ENSG00000291325 (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 (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000707165.1. 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
	ENSG00000291325	ENST00000707165.1		n.260-65698G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0889 AC: 13523 AN: 152102 Hom.: 1008 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0387

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.0471

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0397

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0457

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0889 AC: 13536 AN: 152220 Hom.: 1012 Cov.: 33 AF XY: 0.0885 AC XY: 6588 AN XY: 74452

African (AFR) AF: 0.198 AC: 8199 AN: 41496

American (AMR) AF: 0.0386 AC: 590 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3472

East Asian (EAS) AF: 0.0472 AC: 245 AN: 5186

South Asian (SAS) AF: 0.150 AC: 721 AN: 4820

European-Finnish (FIN) AF: 0.0397 AC: 421 AN: 10616

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0457 AC: 3111 AN: 68010

Other (OTH) AF: 0.0701 AC: 148 AN: 2112

Alfa AF: 0.0558 Hom.: 531

Bravo AF: 0.0894

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.68
PhyloP100		-0.058

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: rs12712001;

hg19: chr2-4420858;