rs36084323

chr2-241859444-C-T

Variant summary

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

The XR_007088436.1(LOC124908032):n.373C>T 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 0.0599 in 152,288 control chromosomes in the GnomAD database, including 1,049 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 0.060 (1049 hom., cov: 33)
• Consequence: LOC124908032 XR_007088436.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

LOC124908032 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124908032	XR_007088436.1	n.373C>T		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9075 AN: 152170 Hom.: 1043 Cov.: 33

Gnomad AFR AF: 0.0464

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.0678

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

GnomAD4 genome AF: 0.0599 AC: 9116 AN: 152288 Hom.: 1049 Cov.: 33 AF XY: 0.0682 AC XY: 5077 AN XY: 74464

Gnomad4 AFR AF: 0.0468

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.0788

Gnomad4 FIN AF: 0.0535

Gnomad4 NFE AF: 0.0118

Gnomad4 OTH AF: 0.0704

Alfa AF: 0.0345 Hom.: 42

Bravo AF: 0.0714

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	8.2
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36084323; hg19: chr2-242801596;