rs11664999

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372017	XR_935279.3	n.324+6389C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264825	ENST00000578741.1	n.224-4629C>T		intron_variant	Intron 1 of 1	3

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 v4.3

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

Other links and lift over

dbSNP: rs11664999; hg19: chr18-19803221;