chr13-40536747-C-T

Variant names:

• chr13-40536747-C-T
• rs2721051
• ENST00000636651.2:n.1459+22762G>A

Variant summary

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

The ENST00000636651.2(ENSG00000288542):​n.1459+22762G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0856 in 152,010 control chromosomes in the GnomAD database, including 625 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 0.086 (625 hom., cov: 30)
• Consequence: ENSG00000288542 ENST00000636651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 49 publications found

Genes affected

ENSG00000288542 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0974 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
ENSG00000288542	ENST00000636651.2	n.1459+22762G>A		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0856 AC: 13000 AN: 151894 Hom.: 623 Cov.: 30

Gnomad AFR AF: 0.0700

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0427

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0994

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.0856 AC: 13009 AN: 152010 Hom.: 625 Cov.: 30 AF XY: 0.0819 AC XY: 6087 AN XY: 74312

African (AFR) AF: 0.0702 AC: 2912 AN: 41476

American (AMR) AF: 0.101 AC: 1537 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3470

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5160

South Asian (SAS) AF: 0.0419 AC: 202 AN: 4820

European-Finnish (FIN) AF: 0.0702 AC: 741 AN: 10556

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.0993 AC: 6751 AN: 67952

Other (OTH) AF: 0.120 AC: 253 AN: 2104

Alfa AF: 0.0979 Hom.: 3277

Bravo AF: 0.0876

Asia WGS AF: 0.0250 AC: 86 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	9.5
DANN	Benign	0.57
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs2721051; hg19: chr13-41110884;