rs10492361

Positions:

• chr12-28080433-A-G

Variant summary

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

The XR_931461.3(LOC105369710):​n.156-16546T>C 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 0.155 in 152,116 control chromosomes in the GnomAD database, including 2,449 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 0.16 (2449 hom., cov: 32)
• Consequence: LOC105369710 XR_931461.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596

Genes affected

LOC105369710 (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 (NFE) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369710	XR_931461.3	n.156-16546T>C		intron_variant, non_coding_transcript_variant
LOC105369710	XR_931462.3	n.8578T>C		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23589 AN: 151998 Hom.: 2450 Cov.: 32

Gnomad AFR AF: 0.0423

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.0755

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.155 AC: 23583 AN: 152116 Hom.: 2449 Cov.: 32 AF XY: 0.150 AC XY: 11169 AN XY: 74318

Gnomad4 AFR AF: 0.0421

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.00387

Gnomad4 SAS AF: 0.0762

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.176

Alfa AF: 0.218 Hom.: 4550

Bravo AF: 0.147

Asia WGS AF: 0.0420 AC: 150 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	1.5
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492361; hg19: chr12-28233366;