2-120551912-C-T

Position:

• chr2-120551912-C-T

Variant summary

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

The XR_002959417.2(LOC105373585):​n.1474G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 152,056 control chromosomes in the GnomAD database, including 14,805 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 0.44 (14805 hom., cov: 32)
• Consequence: LOC105373585 XR_002959417.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

LOC105373585 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373585	XR_002959417.2	n.1474G>A		non_coding_transcript_exon_variant	1/4
LOC105373585	XR_001739681.3	n.2105G>A		non_coding_transcript_exon_variant	3/4
LOC105373585	XR_007087217.1	n.1474G>A		non_coding_transcript_exon_variant	1/2
LOC105373585	XR_007087218.1	n.1474G>A		non_coding_transcript_exon_variant	1/5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66516 AN: 151936 Hom.: 14769 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.438 AC: 66600 AN: 152056 Hom.: 14805 Cov.: 32 AF XY: 0.435 AC XY: 32310 AN XY: 74312

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.452

Alfa AF: 0.417 Hom.: 30362

Bravo AF: 0.445

Asia WGS AF: 0.487 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2030746; hg19: chr2-121309488;