rs12615721

chr2-81629402-G-A

Variant summary

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

The XR_007088668.1(LOC102724542):n.667+49793G>A 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 0.134 in 152,052 control chromosomes in the GnomAD database, including 1,878 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 0.13 (1878 hom., cov: 32)
• Consequence: LOC102724542 XR_007088668.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

Genes affected

LOC102724542 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724542	XR_007088668.1	n.667+49793G>A		intron_variant, non_coding_transcript_variant
LOC102724542	XR_940294.2	n.575+49793G>A		intron_variant, non_coding_transcript_variant
LOC102724542	XR_940295.2	n.497+80655G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20313 AN: 151934 Hom.: 1863 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0742

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.134 AC: 20370 AN: 152052 Hom.: 1878 Cov.: 32 AF XY: 0.131 AC XY: 9762 AN XY: 74356

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.0751

Gnomad4 FIN AF: 0.0436

Gnomad4 NFE AF: 0.0782

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0950 Hom.: 940

Bravo AF: 0.143

Asia WGS AF: 0.133 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.045
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12615721; hg19: chr2-81856526;