rs1992269

Variant names:

• chr18-1872316-C-T
• rs1992269
• ENST00000653094.1:n.526+385C>T

Variant summary

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

The ENST00000653094.1(ENSG00000266602):​n.526+385C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,326 control chromosomes in the GnomAD database, including 5,122 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 0.24 (5122 hom., cov: 32)
• Consequence: ENSG00000266602 ENST00000653094.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

ENSG00000266602 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 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
ENSG00000266602	ENST00000653094.1	n.526+385C>T		intron_variant	Intron 5 of 5
ENSG00000266602	ENST00000653330.1	n.452+385C>T		intron_variant	Intron 4 of 4
ENSG00000266602	ENST00000655815.1	n.452+385C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35751 AN: 151210 Hom.: 5107 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0178

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.237 AC: 35801 AN: 151326 Hom.: 5122 Cov.: 32 AF XY: 0.234 AC XY: 17267 AN XY: 73900

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.0178

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.206

Alfa AF: 0.187 Hom.: 3803

Bravo AF: 0.241

Asia WGS AF: 0.0960 AC: 332 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.46
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1992269; hg19: chr18-1872317;