20-53733353-T-C

Variant names:

• chr20-53733353-T-C
• rs6091737
• ENST00000716917.1:n.504-7051T>C

Variant summary

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

The ENST00000716917.1(ENSG00000293654):​n.504-7051T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,866 control chromosomes in the GnomAD database, including 5,849 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 0.27 (5849 hom., cov: 32)
• Consequence: ENSG00000293654 ENST00000716917.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767
• Publications: 14 publications found

Genes affected

ENSG00000293654 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 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
ENSG00000293654	ENST00000716917.1	n.504-7051T>C		intron_variant	Intron 2 of 2
ENSG00000293654	ENST00000716918.1	n.340-7051T>C		intron_variant	Intron 1 of 1
ENSG00000287886	ENST00000716922.1	n.162-7051T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41538 AN: 151748 Hom.: 5856 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.274 AC: 41541 AN: 151866 Hom.: 5849 Cov.: 32 AF XY: 0.274 AC XY: 20344 AN XY: 74214

African (AFR) AF: 0.243 AC: 10064 AN: 41448

American (AMR) AF: 0.250 AC: 3812 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 781 AN: 3466

East Asian (EAS) AF: 0.497 AC: 2561 AN: 5148

South Asian (SAS) AF: 0.270 AC: 1298 AN: 4816

European-Finnish (FIN) AF: 0.277 AC: 2916 AN: 10540

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19135 AN: 67912

Other (OTH) AF: 0.276 AC: 581 AN: 2102

Alfa AF: 0.282 Hom.: 26512

Bravo AF: 0.270

Asia WGS AF: 0.348 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.78
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs6091737; hg19: chr20-52349892;