rs12529724

Variant names:

• chr6-90824373-G-A
• rs12529724
• XR_001744259.1:n.1244-83683G>A

Variant summary

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

The XR_001744259.1(LOC107986623):​n.1244-83683G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,922 control chromosomes in the GnomAD database, including 4,168 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 0.23 (4168 hom., cov: 32)
• Consequence: LOC107986623 XR_001744259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 4 publications found

Genes affected

LOC107986623 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986623	XR_001744259.1	n.1244-83683G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34752 AN: 151804 Hom.: 4165 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.229 AC: 34759 AN: 151922 Hom.: 4168 Cov.: 32 AF XY: 0.232 AC XY: 17192 AN XY: 74230

African (AFR) AF: 0.159 AC: 6598 AN: 41482

American (AMR) AF: 0.193 AC: 2939 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 628 AN: 3464

East Asian (EAS) AF: 0.220 AC: 1138 AN: 5164

South Asian (SAS) AF: 0.334 AC: 1605 AN: 4810

European-Finnish (FIN) AF: 0.310 AC: 3259 AN: 10520

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17817 AN: 67910

Other (OTH) AF: 0.233 AC: 492 AN: 2110

Alfa AF: 0.246 Hom.: 20845

Bravo AF: 0.213

Asia WGS AF: 0.314 AC: 1093 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.87
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs12529724; hg19: chr6-91534091;