6-90824373-G-A

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;