rs3755132

chr2-15589696-T-G

Variant summary

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

The XR_007086224.1(LOC124905975):n.1947A>C 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 0.256 in 152,154 control chromosomes in the GnomAD database, including 6,593 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 0.26 (6593 hom., cov: 32)
• Consequence: LOC124905975 XR_007086224.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

Genes affected

LOC124905975 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905975	XR_007086224.1	n.1947A>C		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38976 AN: 152036 Hom.: 6588 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.256 AC: 39020 AN: 152154 Hom.: 6593 Cov.: 32 AF XY: 0.254 AC XY: 18875 AN XY: 74388

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.229

Alfa AF: 0.166 Hom.: 4908

Bravo AF: 0.272

Asia WGS AF: 0.251 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.4
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3755132; hg19: chr2-15729820;