rs11664999

chr18-22223258-C-T

Variant summary

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

The ENST00000578741.1(ENSG00000264825):n.224-4629C>T variant causes a intron, non coding transcript 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: ENST00000578741.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105372017	XR_935279.3	n.324+6389C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000578741.1	n.224-4629C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.0749

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.265

Alfa AF: 0.304 Hom.: 3170

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11664999; hg19: chr18-19803221;