rs17700144

Positions:

• chr18-60144750-G-A

Variant summary

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

The ENST00000588794.1(ENSG00000267686):​n.346+15095G>A 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 0.147 in 152,210 control chromosomes in the GnomAD database, including 2,231 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 0.15 (2231 hom., cov: 32)
• Consequence: ENST00000588794.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000588794.1	n.346+15095G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22385 AN: 152092 Hom.: 2228 Cov.: 32

Gnomad AFR AF: 0.0352

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0263

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.147 AC: 22386 AN: 152210 Hom.: 2231 Cov.: 32 AF XY: 0.144 AC XY: 10747 AN XY: 74408

Gnomad4 AFR AF: 0.0351

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.0264

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.163

Alfa AF: 0.170 Hom.: 421

Bravo AF: 0.136

Asia WGS AF: 0.141 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
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: rs17700144; hg19: chr18-57811982;