rs17047718

Positions:

• chr2-118079736-A-G

Variant summary

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

The XR_001739662.3(LOC107985940):​n.181+8515T>C 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 0.0678 in 152,310 control chromosomes in the GnomAD database, including 434 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 0.068 (434 hom., cov: 32)
• Consequence: LOC107985940 XR_001739662.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.940

Genes affected

LOC107985940 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985940	XR_001739662.3	n.181+8515T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0678 AC: 10322 AN: 152192 Hom.: 434 Cov.: 32

Gnomad AFR AF: 0.0425

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0722

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0642

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0678 AC: 10333 AN: 152310 Hom.: 434 Cov.: 32 AF XY: 0.0705 AC XY: 5251 AN XY: 74482

Gnomad4 AFR AF: 0.0425

Gnomad4 AMR AF: 0.0722

Gnomad4 ASJ AF: 0.0542

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0992

Gnomad4 NFE AF: 0.0642

Gnomad4 OTH AF: 0.0737

Alfa AF: 0.0556 Hom.: 38

Bravo AF: 0.0626

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.4
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: rs17047718; hg19: chr2-118837312;