2-45650417-C-T

Variant names:

• chr2-45650417-C-T
• rs608139
• XR_005647118.2:n.797G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_005647118.2(LOC102724965):​n.797G>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 0.838 in 152,242 control chromosomes in the GnomAD database, including 53,463 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 0.84 (53463 hom., cov: 35)
• Consequence: LOC102724965 XR_005647118.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177
• Publications: 6 publications found

Genes affected

LOC102724965 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724965	XR_005647118.2	n.797G>A		non_coding_transcript_exon_variant	Exon 1 of 2
LOC102724965	XR_005647119.2	n.799G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127442 AN: 152124 Hom.: 53449 Cov.: 35

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.838 AC: 127506 AN: 152242 Hom.: 53463 Cov.: 35 AF XY: 0.837 AC XY: 62260 AN XY: 74424

African (AFR) AF: 0.803 AC: 33367 AN: 41530

American (AMR) AF: 0.862 AC: 13197 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3058 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4499 AN: 5166

South Asian (SAS) AF: 0.859 AC: 4144 AN: 4826

European-Finnish (FIN) AF: 0.812 AC: 8607 AN: 10600

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57841 AN: 68014

Other (OTH) AF: 0.835 AC: 1767 AN: 2116

Alfa AF: 0.849 Hom.: 54344

Bravo AF: 0.839

Asia WGS AF: 0.869 AC: 3022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.9
DANN	Benign	0.90
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs608139; hg19: chr2-45877556;