22-39274846-G-T

Variant names:

• chr22-39274846-G-T
• rs968451
• ENST00000641859.1:n.110-1730G>T

Variant summary

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

The ENST00000641859.1(ENSG00000284633):​n.110-1730G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,022 control chromosomes in the GnomAD database, including 4,025 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 0.19 (4025 hom., cov: 31)
• Consequence: ENSG00000284633 ENST00000641859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

Genes affected

ENSG00000284633 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.727 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
ENSG00000284633	ENST00000641859.1	n.110-1730G>T		intron_variant	Intron 1 of 2
ENSG00000284633	ENST00000642075.1	n.383-1730G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28912 AN: 151904 Hom.: 4028 Cov.: 31

Gnomad AFR AF: 0.0716

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.190 AC: 28912 AN: 152022 Hom.: 4025 Cov.: 31 AF XY: 0.201 AC XY: 14906 AN XY: 74264

Gnomad4 AFR AF: 0.0714

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.193

Alfa AF: 0.204 Hom.: 6334

Bravo AF: 0.186

Asia WGS AF: 0.462 AC: 1606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs968451; hg19: chr22-39670851;