13-53727505-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000287722 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657016.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287722	ENST00000657016.1		n.630-19931T>C		intron	N/A

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

African (AFR) AF: 0.0437 AC: 1818 AN: 41588

American (AMR) AF: 0.0356 AC: 543 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0822 AC: 285 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5182

South Asian (SAS) AF: 0.0350 AC: 169 AN: 4830

European-Finnish (FIN) AF: 0.0936 AC: 993 AN: 10614

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0594 AC: 4035 AN: 67974

Other (OTH) AF: 0.0440 AC: 93 AN: 2114

Alfa AF: 0.0507 Hom.: 140

Bravo AF: 0.0477

Asia WGS AF: 0.0180 AC: 63 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.21
DANN	Benign	0.79
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs957940;

hg19: chr13-54301640;