rs12776126

Positions:

• chr10-8095420-G-T

Variant summary

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

The XR_930636.3(LOC105376395):​n.186-657G>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 0.119 in 152,146 control chromosomes in the GnomAD database, including 1,682 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 0.12 (1682 hom., cov: 32)
• Consequence: LOC105376395 XR_930636.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623

Genes affected

LOC105376395 (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 = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376395	XR_930636.3	n.186-657G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18090 AN: 152028 Hom.: 1673 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.0895

Gnomad SAS AF: 0.0282

Gnomad FIN AF: 0.0831

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.0927

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

GnomAD4 genome AF: 0.119 AC: 18130 AN: 152146 Hom.: 1682 Cov.: 32 AF XY: 0.119 AC XY: 8850 AN XY: 74378

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.0895

Gnomad4 SAS AF: 0.0278

Gnomad4 FIN AF: 0.0831

Gnomad4 NFE AF: 0.0561

Gnomad4 OTH AF: 0.0922

Alfa AF: 0.0686 Hom.: 722

Bravo AF: 0.127

Asia WGS AF: 0.0780 AC: 274 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	0.97
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12776126; hg19: chr10-8137383;