chr2-168260515-G-T

Position:

• chr2-168260515-G-T

Variant summary

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

The XR_007087282.1(LOC107985959):​n.109-4581G>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 0.156 in 152,234 control chromosomes in the GnomAD database, including 1,988 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 0.16 (1988 hom., cov: 33)
• Consequence: LOC107985959 XR_007087282.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241

Genes affected

LOC107985959 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985959	XR_007087282.1	n.109-4581G>T		intron_variant, non_coding_transcript_variant
LOC107985959	XR_001739763.2	n.703-4581G>T		intron_variant, non_coding_transcript_variant
LOC107985959	XR_001739765.2	n.227-4581G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23723 AN: 152114 Hom.: 1984 Cov.: 33

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.0962

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.156 AC: 23747 AN: 152234 Hom.: 1988 Cov.: 33 AF XY: 0.155 AC XY: 11525 AN XY: 74428

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.0962

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.170

Alfa AF: 0.0270 Hom.: 198

Bravo AF: 0.166

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2102808; hg19: chr2-169117025;