rs17384005

chr18-1575019-A-G

Variant summary

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

The ENST00000661994.1(ENSG00000266602):n.266+8495A>G 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 0.127 in 152,126 control chromosomes in the GnomAD database, including 1,404 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 0.13 (1404 hom., cov: 32)
• Consequence: ENST00000661994.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661994.1	n.266+8495A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19287 AN: 152008 Hom.: 1401 Cov.: 32

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0896

Gnomad EAS AF: 0.00828

Gnomad SAS AF: 0.0740

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.127 AC: 19301 AN: 152126 Hom.: 1404 Cov.: 32 AF XY: 0.123 AC XY: 9135 AN XY: 74364

Gnomad4 AFR AF: 0.0727

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.0896

Gnomad4 EAS AF: 0.00849

Gnomad4 SAS AF: 0.0743

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.122

Alfa AF: 0.144 Hom.: 395

Bravo AF: 0.125

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.63
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17384005; hg19: chr18-1575020;