rs1992269

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000266602 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653094.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266602	ENST00000653094.1		n.526+385C>T		intron	N/A
	ENSG00000266602	ENST00000653330.1		n.452+385C>T		intron	N/A
	ENSG00000266602	ENST00000655815.1		n.452+385C>T		intron	N/A

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

African (AFR) AF: 0.409 AC: 16847 AN: 41226

American (AMR) AF: 0.178 AC: 2703 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 517 AN: 3456

East Asian (EAS) AF: 0.0178 AC: 92 AN: 5164

South Asian (SAS) AF: 0.145 AC: 696 AN: 4794

European-Finnish (FIN) AF: 0.190 AC: 1984 AN: 10442

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.182 AC: 12317 AN: 67724

Other (OTH) AF: 0.206 AC: 434 AN: 2102

Alfa AF: 0.198 Hom.: 10175

Bravo AF: 0.241

Asia WGS AF: 0.0960 AC: 332 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.46
DANN	Benign	0.33
PhyloP100		-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1992269;

hg19: chr18-1872317;