rs13252644

Variant names:

• chr8-127626894-C-A
• rs13252644
• ENST00000650971.1:n.390-2874C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-127626894-C-A
• chr8-127626894-C-T

Variant summary

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

The ENST00000650971.1(ENSG00000286266):​n.390-2874C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0917 in 152,172 control chromosomes in the GnomAD database, including 863 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 0.092 (863 hom., cov: 32)
• Consequence: ENSG00000286266 ENST00000650971.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.503

Genes affected

ENSG00000286266 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286266	ENST00000650971.1	n.390-2874C>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0916 AC: 13921 AN: 152054 Hom.: 860 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.0207

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0582

Gnomad OTH AF: 0.0774

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

GnomAD4 genome AF: 0.0917 AC: 13959 AN: 152172 Hom.: 863 Cov.: 32 AF XY: 0.0926 AC XY: 6894 AN XY: 74410

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.0207

Gnomad4 FIN AF: 0.0848

Gnomad4 NFE AF: 0.0582

Gnomad4 OTH AF: 0.0775

Alfa AF: 0.0738 Hom.: 267

Bravo AF: 0.0999

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13252644; hg19: chr8-128639139;