rs8024343

Variant names:

• chr15-87166835-A-T
• rs8024343
• XR_932582.2:n.167-11392A>T

Variant summary

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

The XR_932582.2(LOC105370955):​n.167-11392A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,152 control chromosomes in the GnomAD database, including 1,634 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 0.14 (1634 hom., cov: 32)
• Consequence: LOC105370955 XR_932582.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 2 publications found

Genes affected

LOC105370955 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.161 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: 0.144 AC: 21905 AN: 152034 Hom.: 1627 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.144 AC: 21919 AN: 152152 Hom.: 1634 Cov.: 32 AF XY: 0.144 AC XY: 10714 AN XY: 74396

African (AFR) AF: 0.107 AC: 4436 AN: 41516

American (AMR) AF: 0.166 AC: 2530 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 677 AN: 3464

East Asian (EAS) AF: 0.109 AC: 560 AN: 5152

South Asian (SAS) AF: 0.171 AC: 822 AN: 4818

European-Finnish (FIN) AF: 0.134 AC: 1425 AN: 10596

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10982 AN: 68002

Other (OTH) AF: 0.157 AC: 333 AN: 2116

Alfa AF: 0.150 Hom.: 223

Bravo AF: 0.147

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.39
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs8024343; hg19: chr15-87710066;