rs12084589

Variant names:

• chr1-159718651-C-A
• rs12084589
• ENST00000751816.1:n.108-7876C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-159718651-C-A
• chr1-159718651-C-T

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-7876C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,266 control chromosomes in the GnomAD database, including 2,255 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 0.14 (2255 hom., cov: 34)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 4 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 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
ENSG00000297913	ENST00000751816.1	n.108-7876C>A		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-7876C>A		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-7876C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20566 AN: 152148 Hom.: 2247 Cov.: 34

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.135 AC: 20600 AN: 152266 Hom.: 2255 Cov.: 34 AF XY: 0.134 AC XY: 9958 AN XY: 74458

African (AFR) AF: 0.301 AC: 12499 AN: 41536

American (AMR) AF: 0.0774 AC: 1185 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3470

East Asian (EAS) AF: 0.153 AC: 790 AN: 5180

South Asian (SAS) AF: 0.102 AC: 490 AN: 4822

European-Finnish (FIN) AF: 0.0650 AC: 690 AN: 10618

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.0614 AC: 4175 AN: 68020

Other (OTH) AF: 0.129 AC: 272 AN: 2112

Alfa AF: 0.131 Hom.: 319

Bravo AF: 0.142

Asia WGS AF: 0.109 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.12
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs12084589; hg19: chr1-159688441;