rs12529724

chr6-90824373-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001744259.1(LOC107986623):n.1244-83683G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

LOC107986623 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107986623	XR_001744259.1	n.1244-83683G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.233

Alfa AF: 0.249 Hom.: 9591

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12529724; hg19: chr6-91534091;