4-23702024-T-G

Variant names:

• chr4-23702024-T-G
• rs1038821
• ENST00000514290.1:n.118-66295T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000514290.1(ENSG00000250137):​n.118-66295T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 152,160 control chromosomes in the GnomAD database, including 13,458 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 0.40 (13458 hom., cov: 33)
• Consequence: ENSG00000250137 ENST00000514290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

ENSG00000250137 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 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
ENSG00000250137	ENST00000514290.1	n.118-66295T>G		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61270 AN: 152042 Hom.: 13462 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.403 AC: 61273 AN: 152160 Hom.: 13458 Cov.: 33 AF XY: 0.399 AC XY: 29703 AN XY: 74392

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.426

Alfa AF: 0.357 Hom.: 1508

Bravo AF: 0.394

Asia WGS AF: 0.303 AC: 1057 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	0.67
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1038821; hg19: chr4-23703647;