chr13-53340886-C-G

Variant names:

• chr13-53340886-C-G
• rs1418617
• ENST00000657016.1:n.629+36764C>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000657016.1(ENSG00000287722):​n.629+36764C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,034 control chromosomes in the GnomAD database, including 14,464 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 (14464 hom., cov: 33)
• Consequence: ENSG00000287722 ENST00000657016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.51
• Publications: 3 publications found

Genes affected

ENSG00000287722 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.516 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
ENSG00000287722	ENST00000657016.1	n.629+36764C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65570 AN: 151916 Hom.: 14458 Cov.: 33

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.431 AC: 65600 AN: 152034 Hom.: 14464 Cov.: 33 AF XY: 0.436 AC XY: 32373 AN XY: 74304

African (AFR) AF: 0.365 AC: 15133 AN: 41470

American (AMR) AF: 0.526 AC: 8038 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1637 AN: 3470

East Asian (EAS) AF: 0.431 AC: 2228 AN: 5166

South Asian (SAS) AF: 0.461 AC: 2223 AN: 4820

European-Finnish (FIN) AF: 0.472 AC: 4976 AN: 10550

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29786 AN: 67946

Other (OTH) AF: 0.457 AC: 967 AN: 2114

Alfa AF: 0.441 Hom.: 1856

Bravo AF: 0.434

Asia WGS AF: 0.442 AC: 1536 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	13
DANN	Benign	0.60
PhyloP100		3.5

Splicing

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

Other links and lift over

dbSNP: rs1418617; hg19: chr13-53915021;