chr22-36466454-T-C

Variant names:

• chr22-36466454-T-C
• rs139998
• ENST00000750843.1:n.*38T>C

Variant summary

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

The ENST00000750843.1(ENSG00000297762):​n.*38T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,108 control chromosomes in the GnomAD database, including 9,672 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 0.31 (9672 hom., cov: 33)
• Consequence: ENSG00000297762 ENST00000750843.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.04
• Publications: 7 publications found

Genes affected

ENSG00000297762 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 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
ENSG00000297762	ENST00000750843.1	n.*38T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46904 AN: 151990 Hom.: 9654 Cov.: 33

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.309 AC: 46972 AN: 152108 Hom.: 9672 Cov.: 33 AF XY: 0.306 AC XY: 22749 AN XY: 74368

African (AFR) AF: 0.592 AC: 24566 AN: 41480

American (AMR) AF: 0.174 AC: 2668 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1008 AN: 3470

East Asian (EAS) AF: 0.138 AC: 711 AN: 5170

South Asian (SAS) AF: 0.236 AC: 1139 AN: 4822

European-Finnish (FIN) AF: 0.229 AC: 2430 AN: 10590

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13548 AN: 67966

Other (OTH) AF: 0.263 AC: 556 AN: 2114

Alfa AF: 0.221 Hom.: 7450

Bravo AF: 0.313

Asia WGS AF: 0.219 AC: 762 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	0.0060
DANN	Benign	0.35
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs139998; hg19: chr22-36862501;