rs12130862

Variant names:

• chr1-152054539-A-T
• rs12130862
• ENST00000759538.1:n.958+8230A>T

Variant summary

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

The ENST00000759538.1(ENSG00000229021):​n.958+8230A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,248 control chromosomes in the GnomAD database, including 2,245 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 0.15 (2245 hom., cov: 32)
• Consequence: ENSG00000229021 ENST00000759538.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70
• Publications: 7 publications found

Genes affected

ENSG00000229021 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000759538.1. 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
	ENSG00000229021	ENST00000759538.1		n.958+8230A>T		intron	N/A
	ENSG00000229021	ENST00000759539.1		n.49+1690A>T		intron	N/A
	ENSG00000229021	ENST00000759540.1		n.49+1690A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22155 AN: 152130 Hom.: 2243 Cov.: 32

Gnomad AFR AF: 0.0409

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.145 AC: 22147 AN: 152248 Hom.: 2245 Cov.: 32 AF XY: 0.147 AC XY: 10927 AN XY: 74438

African (AFR) AF: 0.0408 AC: 1695 AN: 41564

American (AMR) AF: 0.115 AC: 1760 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 421 AN: 3472

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5188

South Asian (SAS) AF: 0.122 AC: 592 AN: 4834

European-Finnish (FIN) AF: 0.286 AC: 3032 AN: 10588

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14202 AN: 67984

Other (OTH) AF: 0.148 AC: 313 AN: 2110

Alfa AF: 0.190 Hom.: 397

Bravo AF: 0.125

Asia WGS AF: 0.0590 AC: 207 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.8
DANN	Benign	0.72
PhyloP100		1.7

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: rs12130862;

hg19: chr1-152027015;