22-19750832-C-T

Variant names:

• chr22-19750832-C-T
• rs1005133
• ENST00000755342.1:n.84-183C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000755342.1(ENSG00000298407):​n.84-183C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 147,064 control chromosomes in the GnomAD database, including 3,889 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 0.21 (3889 hom., cov: 22)
• Consequence: ENSG00000298407 ENST00000755342.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 5 publications found

Genes affected

ENSG00000298407 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 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
ENSG00000298407	ENST00000755342.1	n.84-183C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.206 AC: 30343 AN: 146946 Hom.: 3895 Cov.: 22

Gnomad AFR AF: 0.0570

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.206 AC: 30330 AN: 147064 Hom.: 3889 Cov.: 22 AF XY: 0.208 AC XY: 14869 AN XY: 71464

African (AFR) AF: 0.0570 AC: 2268 AN: 39804

American (AMR) AF: 0.232 AC: 3432 AN: 14786

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1212 AN: 3420

East Asian (EAS) AF: 0.473 AC: 2260 AN: 4778

South Asian (SAS) AF: 0.242 AC: 1093 AN: 4522

European-Finnish (FIN) AF: 0.230 AC: 2304 AN: 10008

Middle Eastern (MID) AF: 0.246 AC: 68 AN: 276

European-Non Finnish (NFE) AF: 0.254 AC: 16918 AN: 66542

Other (OTH) AF: 0.228 AC: 466 AN: 2048

Alfa AF: 0.253 Hom.: 8532

Bravo AF: 0.204

Asia WGS AF: 0.277 AC: 964 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	16
DANN	Benign	0.74
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1005133; hg19: chr22-19738355;