2-118086902-C-G

Position:

• chr2-118086902-C-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+1349G>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 0.318 in 152,020 control chromosomes in the GnomAD database, including 7,814 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 0.32 (7814 hom., cov: 33)
• Consequence: LOC107985940 XR_001739662.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555

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 (NFE) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985940	XR_001739662.3	n.181+1349G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48310 AN: 151902 Hom.: 7807 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.318 AC: 48356 AN: 152020 Hom.: 7814 Cov.: 33 AF XY: 0.322 AC XY: 23911 AN XY: 74294

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.303

Alfa AF: 0.341 Hom.: 1216

Bravo AF: 0.307

Asia WGS AF: 0.267 AC: 931 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.62
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10185316; hg19: chr2-118844478; COSMIC: COSV55522182;