rs12623288

chr2-46407506-G-Achr2-46407506-G-C

Variant summary

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

The XR_007086306.1(LOC124907762):n.3363-1281C>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 0.218 in 152,170 control chromosomes in the GnomAD database, including 5,794 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 0.22 (5794 hom., cov: 33)
• Consequence: LOC124907762 XR_007086306.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

LOC124907762 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124907762	XR_007086306.1	n.3363-1281C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33050 AN: 152052 Hom.: 5756 Cov.: 33

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.0746

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.218 AC: 33138 AN: 152170 Hom.: 5794 Cov.: 33 AF XY: 0.219 AC XY: 16297 AN XY: 74380

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.0746

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.0878

Gnomad4 OTH AF: 0.205

Alfa AF: 0.122 Hom.: 3853

Bravo AF: 0.239

Asia WGS AF: 0.377 AC: 1308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.60
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12623288; hg19: chr2-46634645;