chr13-23956756-A-G

Position:

• chr13-23956756-A-G

Variant summary

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

The ENST00000655811.1(ENSG00000287530):​n.122-1847A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,970 control chromosomes in the GnomAD database, including 15,228 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 0.43 (15228 hom., cov: 32)
• Consequence: ENSG00000287530 ENST00000655811.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

Genes affected

ENSG00000287530 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370115	XR_001749789.2	n.163-541A>G		intron_variant
LOC105370115	XR_001749790.2	n.163-544A>G		intron_variant
LOC105370115	XR_001749791.2	n.163-541A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287530	ENST00000655811.1	n.122-1847A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65978 AN: 151850 Hom.: 15188 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.435 AC: 66082 AN: 151970 Hom.: 15228 Cov.: 32 AF XY: 0.436 AC XY: 32417 AN XY: 74272

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.462

Alfa AF: 0.397 Hom.: 10417

Bravo AF: 0.460

Asia WGS AF: 0.442 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.70
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: rs2765119; hg19: chr13-24530895;