rs13262822

Variant names:

• chr8-86209259-G-C
• rs13262822
• ENST00000523112.1:n.460-2936G>C

Your query was ambiguous. Multiple possible variants found:

• chr8-86209259-G-C
• chr8-86209259-G-T

Variant summary

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

The ENST00000523112.1(ENSG00000253699):​n.460-2936G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 151,732 control chromosomes in the GnomAD database, including 9,387 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 0.34 (9387 hom., cov: 32)
• Consequence: ENSG00000253699 ENST00000523112.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

Genes affected

ENSG00000253699 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375623	NR_188044.1	n.410-2936G>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253699	ENST00000523112.1	n.460-2936G>C		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51740 AN: 151612 Hom.: 9349 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.342 AC: 51841 AN: 151732 Hom.: 9387 Cov.: 32 AF XY: 0.349 AC XY: 25878 AN XY: 74116

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.344

Alfa AF: 0.193 Hom.: 402

Bravo AF: 0.348

Asia WGS AF: 0.462 AC: 1605 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13262822; hg19: chr8-87221488;