rs1508595

Variant names:

• chr12-88592239-G-A
• rs1508595
• ENST00000625763.1:n.223-5709G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-88592239-G-A
• chr12-88592239-G-C
• chr12-88592239-G-T

Variant summary

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

The ENST00000625763.1(ENSG00000281333):​n.223-5709G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,898 control chromosomes in the GnomAD database, including 10,777 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 0.30 (10777 hom., cov: 32)
• Consequence: ENSG00000281333 ENST00000625763.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 26 publications found

Genes affected

ENSG00000281333 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000625763.1. 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
	LOC105369885	NR_188177.1		n.218-5709G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000281333	ENST00000625763.1	TSL:2	n.223-5709G>A		intron	N/A
	ENSG00000281333	ENST00000670029.2		n.223-5709G>A		intron	N/A
	ENSG00000281333	ENST00000716318.1		n.218-8055G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46168 AN: 151778 Hom.: 10736 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.305 AC: 46263 AN: 151898 Hom.: 10777 Cov.: 32 AF XY: 0.298 AC XY: 22132 AN XY: 74240

African (AFR) AF: 0.662 AC: 27426 AN: 41414

American (AMR) AF: 0.189 AC: 2878 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3462

East Asian (EAS) AF: 0.279 AC: 1439 AN: 5160

South Asian (SAS) AF: 0.176 AC: 845 AN: 4812

European-Finnish (FIN) AF: 0.134 AC: 1418 AN: 10552

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11058 AN: 67930

Other (OTH) AF: 0.258 AC: 545 AN: 2114

Alfa AF: 0.193 Hom.: 2328

Bravo AF: 0.326

Asia WGS AF: 0.263 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		0.092

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: rs1508595;

hg19: chr12-88986016;