rs12036618

Variant names:

• chr1-111321708-G-A
• rs12036618
• ENST00000426321.2:n.391+2126C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-111321708-G-A
• chr1-111321708-G-T

Variant summary

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

The ENST00000426321.2(ENSG00000229283):​n.391+2126C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 151,980 control chromosomes in the GnomAD database, including 5,458 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 0.25 (5458 hom., cov: 31)
• Consequence: ENSG00000229283 ENST00000426321.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56
• Publications: 5 publications found

Genes affected

ENSG00000229283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.36 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
ENSG00000229283	ENST00000426321.2	n.391+2126C>T		intron_variant	Intron 3 of 3	3
ENSG00000229283	ENST00000725074.1	n.369+2126C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38214 AN: 151862 Hom.: 5461 Cov.: 31

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.251 AC: 38208 AN: 151980 Hom.: 5458 Cov.: 31 AF XY: 0.253 AC XY: 18828 AN XY: 74286

African (AFR) AF: 0.129 AC: 5332 AN: 41482

American (AMR) AF: 0.194 AC: 2958 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1163 AN: 3470

East Asian (EAS) AF: 0.341 AC: 1762 AN: 5164

South Asian (SAS) AF: 0.374 AC: 1795 AN: 4800

European-Finnish (FIN) AF: 0.323 AC: 3397 AN: 10524

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.307 AC: 20857 AN: 67952

Other (OTH) AF: 0.244 AC: 515 AN: 2110

Alfa AF: 0.249 Hom.: 877

Bravo AF: 0.233

Asia WGS AF: 0.316 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.34
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs12036618; hg19: chr1-111864330;