ENST00000653824.3:n.220+39563C>T

Variant names:

• chr1-166205617-C-T
• rs10753713
• ENST00000653824.3:n.220+39563C>T

Variant summary

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

The ENST00000653824.3(ENSG00000229588):​n.220+39563C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,072 control chromosomes in the GnomAD database, including 3,978 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 0.23 (3978 hom., cov: 32)
• Consequence: ENSG00000229588 ENST00000653824.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17
• Publications: 1 publications found

Genes affected

ENSG00000229588 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268276	XR_002958633.2	n.178+39563C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229588	ENST00000653824.3	n.220+39563C>T		intron_variant	Intron 1 of 2
ENSG00000229588	ENST00000829274.1	n.178+39563C>T		intron_variant	Intron 1 of 1
ENSG00000229588	ENST00000829275.1	n.189+39563C>T		intron_variant	Intron 1 of 1
ENSG00000229588	ENST00000829276.1	n.140+39563C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34178 AN: 151952 Hom.: 3965 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.225 AC: 34219 AN: 152072 Hom.: 3978 Cov.: 32 AF XY: 0.227 AC XY: 16905 AN XY: 74346

African (AFR) AF: 0.224 AC: 9298 AN: 41456

American (AMR) AF: 0.215 AC: 3278 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3466

East Asian (EAS) AF: 0.403 AC: 2081 AN: 5164

South Asian (SAS) AF: 0.352 AC: 1699 AN: 4822

European-Finnish (FIN) AF: 0.203 AC: 2147 AN: 10580

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13831 AN: 67998

Other (OTH) AF: 0.267 AC: 560 AN: 2100

Alfa AF: 0.218 Hom.: 1993

Bravo AF: 0.222

Asia WGS AF: 0.358 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.0
DANN	Benign	0.58
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs10753713; hg19: chr1-166174854;