ENST00000425290.1:n.159+5019T>C

Variant names:

• chr10-62800710-A-G
• rs1444418
• ENST00000425290.1:n.159+5019T>C

Variant summary

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

The ENST00000425290.1(ENSG00000238280):​n.159+5019T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,088 control chromosomes in the GnomAD database, including 4,768 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 0.22 (4768 hom., cov: 32)
• Consequence: ENSG00000238280 ENST00000425290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 12 publications found

Genes affected

ENSG00000238280 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 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
ENSG00000238280	ENST00000425290.1	n.159+5019T>C		intron_variant	Intron 1 of 2	5
ENSG00000238280	ENST00000649548.2	n.159+5019T>C		intron_variant	Intron 1 of 3
ENSG00000238280	ENST00000821260.1	n.164+5019T>C		intron_variant	Intron 1 of 1
ENSG00000238280	ENST00000821261.1	n.425+4409T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33535 AN: 151968 Hom.: 4747 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.221 AC: 33621 AN: 152088 Hom.: 4768 Cov.: 32 AF XY: 0.223 AC XY: 16580 AN XY: 74336

African (AFR) AF: 0.378 AC: 15669 AN: 41456

American (AMR) AF: 0.286 AC: 4380 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3470

East Asian (EAS) AF: 0.322 AC: 1663 AN: 5168

South Asian (SAS) AF: 0.163 AC: 785 AN: 4818

European-Finnish (FIN) AF: 0.191 AC: 2025 AN: 10592

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8080 AN: 67978

Other (OTH) AF: 0.212 AC: 448 AN: 2112

Alfa AF: 0.151 Hom.: 9180

Bravo AF: 0.239

Asia WGS AF: 0.268 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.47
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1444418; hg19: chr10-64560470;