13-53727505-T-C

Variant names:

• chr13-53727505-T-C
• rs957940
• ENST00000657016.1:n.630-19931T>C

Variant summary

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

The ENST00000657016.1(ENSG00000287722):​n.630-19931T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0526 in 152,248 control chromosomes in the GnomAD database, including 243 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 0.053 (243 hom., cov: 33)
• Consequence: ENSG00000287722 ENST00000657016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

ENSG00000287722 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0578 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.630-19931T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0526 AC: 7998 AN: 152130 Hom.: 242 Cov.: 33

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0358

Gnomad ASJ AF: 0.0822

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0343

Gnomad FIN AF: 0.0936

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0593

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0526 AC: 8001 AN: 152248 Hom.: 243 Cov.: 33 AF XY: 0.0534 AC XY: 3975 AN XY: 74446

Gnomad4 AFR AF: 0.0437

Gnomad4 AMR AF: 0.0356

Gnomad4 ASJ AF: 0.0822

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0350

Gnomad4 FIN AF: 0.0936

Gnomad4 NFE AF: 0.0594

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0504 Hom.: 126

Bravo AF: 0.0477

Asia WGS AF: 0.0180 AC: 63 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.21
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs957940; hg19: chr13-54301640;