rs12989701

Variant names:

• chr2-127130409-C-A
• rs12989701
• ENST00000726607.1:n.342-4851C>A

Variant summary

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

The ENST00000726607.1(ENSG00000294899):​n.342-4851C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,242 control chromosomes in the GnomAD database, including 1,337 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 0.13 (1337 hom., cov: 32)
• Consequence: ENSG00000294899 ENST00000726607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 45 publications found

Genes affected

ENSG00000294899 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373605	XR_923310.3	n.449-2829C>A		intron_variant	Intron 2 of 3
LOC105373605	XR_923311.4	n.846-2829C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294899	ENST00000726607.1	n.342-4851C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19381 AN: 152124 Hom.: 1334 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.127 AC: 19398 AN: 152242 Hom.: 1337 Cov.: 32 AF XY: 0.124 AC XY: 9250 AN XY: 74450

African (AFR) AF: 0.117 AC: 4864 AN: 41546

American (AMR) AF: 0.0995 AC: 1521 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3472

East Asian (EAS) AF: 0.0106 AC: 55 AN: 5192

South Asian (SAS) AF: 0.0732 AC: 353 AN: 4824

European-Finnish (FIN) AF: 0.140 AC: 1485 AN: 10594

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10336 AN: 68008

Other (OTH) AF: 0.123 AC: 261 AN: 2116

Alfa AF: 0.140 Hom.: 5338

Bravo AF: 0.123

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.61
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12989701; hg19: chr2-127887985;