ENST00000690022.1:n.244-4223C>T

Variant names:

• chr7-128225763-G-A
• rs791600
• ENST00000690022.1:n.244-4223C>T

Variant summary

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

The ENST00000690022.1(ENSG00000289434):​n.244-4223C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,962 control chromosomes in the GnomAD database, including 12,768 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 0.40 (12768 hom., cov: 32)
• Consequence: ENSG00000289434 ENST00000690022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565

Genes affected

ENSG00000289434 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 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
ENSG00000289434	ENST00000690022.1	n.244-4223C>T		intron_variant	Intron 2 of 2
ENSG00000289434	ENST00000692614.2	n.520-4223C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61294 AN: 151842 Hom.: 12763 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.426

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.404 AC: 61325 AN: 151962 Hom.: 12768 Cov.: 32 AF XY: 0.405 AC XY: 30063 AN XY: 74268

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.429

Alfa AF: 0.409 Hom.: 19479

Bravo AF: 0.397

Asia WGS AF: 0.536 AC: 1860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs791600; hg19: chr7-127865816;