chr18-22223258-C-T

Variant names:

• chr18-22223258-C-T
• rs11664999
• ENST00000578741.1:n.224-4629C>T

Variant summary

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

The ENST00000578741.1(ENSG00000264825):​n.224-4629C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,182 control chromosomes in the GnomAD database, including 5,672 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 0.26 (5672 hom., cov: 32)
• Consequence: ENSG00000264825 ENST00000578741.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 3 publications found

Genes affected

ENSG00000264825 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000578741.1. 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
	ENSG00000264825	ENST00000578741.1	TSL:3	n.224-4629C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39535 AN: 152064 Hom.: 5668 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.0749

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.260 AC: 39536 AN: 152182 Hom.: 5672 Cov.: 32 AF XY: 0.253 AC XY: 18831 AN XY: 74380

African (AFR) AF: 0.165 AC: 6833 AN: 41520

American (AMR) AF: 0.232 AC: 3548 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1239 AN: 3468

East Asian (EAS) AF: 0.0749 AC: 388 AN: 5182

South Asian (SAS) AF: 0.283 AC: 1363 AN: 4822

European-Finnish (FIN) AF: 0.270 AC: 2858 AN: 10588

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22491 AN: 67998

Other (OTH) AF: 0.265 AC: 559 AN: 2110

Alfa AF: 0.301 Hom.: 3702

Bravo AF: 0.254

Asia WGS AF: 0.176 AC: 611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.2
DANN	Benign	0.77
PhyloP100		-0.27

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: rs11664999;

hg19: chr18-19803221;