rs263936

Variant names:

• chr13-21643437-C-T
• rs263936
• ENST00000701135.2:n.278-669G>A

Variant summary

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

The ENST00000701135.2(ENSG00000289860):​n.278-669G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,856 control chromosomes in the GnomAD database, including 24,698 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 0.56 (24698 hom., cov: 31)
• Consequence: ENSG00000289860 ENST00000701135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 4 publications found

Genes affected

ENSG00000289860 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 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
ENSG00000289860	ENST00000701135.2	n.278-669G>A		intron_variant	Intron 2 of 2
ENSG00000289860	ENST00000753720.1	n.311-669G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84351 AN: 151738 Hom.: 24654 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.556 AC: 84450 AN: 151856 Hom.: 24698 Cov.: 31 AF XY: 0.548 AC XY: 40678 AN XY: 74192

African (AFR) AF: 0.750 AC: 31096 AN: 41448

American (AMR) AF: 0.405 AC: 6181 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1519 AN: 3470

East Asian (EAS) AF: 0.417 AC: 2137 AN: 5126

South Asian (SAS) AF: 0.591 AC: 2845 AN: 4814

European-Finnish (FIN) AF: 0.441 AC: 4648 AN: 10532

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.505 AC: 34324 AN: 67906

Other (OTH) AF: 0.555 AC: 1169 AN: 2106

Alfa AF: 0.521 Hom.: 14550

Bravo AF: 0.565

Asia WGS AF: 0.521 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.37
DANN	Benign	0.62
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs263936; hg19: chr13-22217576;