rs13000916

chr2-10432727-A-Cchr2-10432727-A-Gchr2-10432727-A-T

Variant summary

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

The XR_007086214.1(LOC124907732):n.87T>G 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 0.65 in 152,104 control chromosomes in the GnomAD database, including 34,072 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 0.65 (34072 hom., cov: 34)
• Consequence: LOC124907732 XR_007086214.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71

Genes affected

LOC124907732 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124907732	XR_007086214.1	n.87T>G		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98755 AN: 151986 Hom.: 34025 Cov.: 34

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.650 AC: 98858 AN: 152104 Hom.: 34072 Cov.: 34 AF XY: 0.651 AC XY: 48420 AN XY: 74358

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.592

Alfa AF: 0.493 Hom.: 1353

Bravo AF: 0.635

Asia WGS AF: 0.538 AC: 1871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.45
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13000916; hg19: chr2-10572853;