rs12712001

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000291325 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000291325	ENST00000707165.1	n.260-65698G>A		intron_variant	Intron 1 of 5

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

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.0386

Gnomad4 ASJ AF: 0.0202

Gnomad4 EAS AF: 0.0472

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0397

Gnomad4 NFE AF: 0.0457

Gnomad4 OTH AF: 0.0701

Alfa AF: 0.0521 Hom.: 343

Bravo AF: 0.0894

Asia WGS AF: 0.111 AC: 388 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	2.2
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12712001; hg19: chr2-4420858;