rs11664559

Variant names:

• chr18-14294025-G-A
• rs11664559
• ENST00000577614.2:n.1897+43618G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-14294025-G-A
• chr18-14294025-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000577614.2(ENSG00000283294):​n.1897+43618G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00201 in 144,086 control chromosomes in the GnomAD database, including 54 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 0.0020 (54 hom., cov: 28)
• Consequence: ENSG00000283294 ENST00000577614.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784

Genes affected

ENSG00000283294 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BS2: High Homozygotes in GnomAd4 at 54 gene

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
ENSG00000283294	ENST00000577614.2	n.1897+43618G>A		intron_variant	Intron 9 of 12	5

Frequencies

GnomAD3 genomes AF: 0.00201 AC: 289 AN: 143968 Hom.: 54 Cov.: 28

Gnomad AFR AF: 0.000709

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000970

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000646

Gnomad FIN AF: 0.000522

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00374

Gnomad OTH AF: 0.00103

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

GnomAD4 genome AF: 0.00201 AC: 290 AN: 144086 Hom.: 54 Cov.: 28 AF XY: 0.00175 AC XY: 123 AN XY: 70180

Gnomad4 AFR AF: 0.000707

Gnomad4 AMR AF: 0.000969

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000862

Gnomad4 FIN AF: 0.000522

Gnomad4 NFE AF: 0.00374

Gnomad4 OTH AF: 0.00102

Alfa AF: 0.000652 Hom.: 107

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11664559; hg19: chr18-14294024;