rs17047731

chr2-118083157-G-A

Variant summary

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

The XR_001739662.3(LOC107985940):n.181+5094C>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 0.0876 in 152,056 control chromosomes in the GnomAD database, including 640 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 0.088 (640 hom., cov: 32)
• Consequence: LOC107985940 XR_001739662.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.614

Genes affected

LOC107985940 (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 (EAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985940	XR_001739662.3	n.181+5094C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0875 AC: 13291 AN: 151938 Hom.: 640 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.0855

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0665

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.0876 AC: 13315 AN: 152056 Hom.: 640 Cov.: 32 AF XY: 0.0897 AC XY: 6666 AN XY: 74314

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.0855

Gnomad4 ASJ AF: 0.0568

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0664

Gnomad4 OTH AF: 0.0866

Alfa AF: 0.0738 Hom.: 74

Bravo AF: 0.0833

Asia WGS AF: 0.166 AC: 574 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.8
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17047731; hg19: chr2-118840733;