rs17083844

chr18-71175007-G-A

Variant summary

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

The ENST00000658819.1(ENSG00000287693):n.192-22931G>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 0.0698 in 152,096 control chromosomes in the GnomAD database, including 590 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 0.070 (590 hom., cov: 32)
• Consequence: ENST00000658819.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209

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 (AFR) allele frequency at 95% confidence interval = 0.14 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
	ENST00000658819.1	n.192-22931G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0696 AC: 10584 AN: 151978 Hom.: 583 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.0253

Gnomad EAS AF: 0.0610

Gnomad SAS AF: 0.0545

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0317

Gnomad OTH AF: 0.0725

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

GnomAD4 genome AF: 0.0698 AC: 10620 AN: 152096 Hom.: 590 Cov.: 32 AF XY: 0.0697 AC XY: 5181 AN XY: 74362

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.0935

Gnomad4 ASJ AF: 0.0253

Gnomad4 EAS AF: 0.0613

Gnomad4 SAS AF: 0.0545

Gnomad4 FIN AF: 0.0231

Gnomad4 NFE AF: 0.0317

Gnomad4 OTH AF: 0.0726

Alfa AF: 0.0387 Hom.: 256

Bravo AF: 0.0794

Asia WGS AF: 0.0920 AC: 317 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	2.4
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17083844; hg19: chr18-68842243;