chr20-5356895-T-C

Variant names:

• chr20-5356895-T-C
• rs1028555
• ENST00000668553.1:n.1120+35723T>C

Variant summary

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

The ENST00000668553.1(ENSG00000230563):​n.1120+35723T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,034 control chromosomes in the GnomAD database, including 14,051 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 (14051 hom., cov: 32)
• Consequence: ENSG00000230563 ENST00000668553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.769
• Publications: 3 publications found

Genes affected

ENSG00000230563 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 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
ENSG00000230563	ENST00000668553.1	n.1120+35723T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65142 AN: 151916 Hom.: 14032 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.429 AC: 65209 AN: 152034 Hom.: 14051 Cov.: 32 AF XY: 0.428 AC XY: 31817 AN XY: 74332

African (AFR) AF: 0.367 AC: 15192 AN: 41448

American (AMR) AF: 0.462 AC: 7055 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1762 AN: 3468

East Asian (EAS) AF: 0.491 AC: 2539 AN: 5168

South Asian (SAS) AF: 0.451 AC: 2174 AN: 4822

European-Finnish (FIN) AF: 0.403 AC: 4256 AN: 10562

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30746 AN: 67970

Other (OTH) AF: 0.456 AC: 963 AN: 2114

Alfa AF: 0.445 Hom.: 9174

Bravo AF: 0.432

Asia WGS AF: 0.479 AC: 1666 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.53
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs1028555; hg19: chr20-5337541;