rs263936

Positions:

• chr13-21643437-C-T

Variant summary

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

The ENST00000701135.1(ENSG00000289860):​n.278-669G>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 0.556 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: ENST00000701135.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000701135.1	n.278-669G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.555

Alfa AF: 0.518 Hom.: 9371

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs263936; hg19: chr13-22217576;