ENST00000429420.1:n.212-1398G>T

Variant names:

• chr10-100338436-C-A
• rs7088953
• ENST00000429420.1:n.212-1398G>T

Variant summary

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

The ENST00000429420.1(ENSG00000231188):​n.212-1398G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0777 in 152,204 control chromosomes in the GnomAD database, including 1,283 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 0.078 (1283 hom., cov: 32)
• Consequence: ENSG00000231188 ENST00000429420.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373
• Publications: 5 publications found

Genes affected

ENSG00000231188 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 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
ENSG00000231188	ENST00000429420.1	n.212-1398G>T		intron_variant	Intron 2 of 3	3
ENSG00000231188	ENST00000775829.1	n.128+825G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0776 AC: 11796 AN: 152086 Hom.: 1283 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0261

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.0715

Gnomad SAS AF: 0.0766

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00403

Gnomad OTH AF: 0.0527

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

GnomAD4 genome AF: 0.0777 AC: 11819 AN: 152204 Hom.: 1283 Cov.: 32 AF XY: 0.0756 AC XY: 5629 AN XY: 74430

African (AFR) AF: 0.247 AC: 10264 AN: 41498

American (AMR) AF: 0.0260 AC: 397 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3472

East Asian (EAS) AF: 0.0717 AC: 371 AN: 5174

South Asian (SAS) AF: 0.0771 AC: 372 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10618

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.00403 AC: 274 AN: 68012

Other (OTH) AF: 0.0550 AC: 116 AN: 2108

Alfa AF: 0.0287 Hom.: 325

Bravo AF: 0.0851

Asia WGS AF: 0.0910 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.65
DANN	Benign	0.56
PhyloP100		-0.37
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7088953; hg19: chr10-102098193;