10-114021768-T-C

Position:

• chr10-114021768-T-C

Variant summary

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

The XR_946332.1(LOC105378492):​n.306-737T>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 0.668 in 152,040 control chromosomes in the GnomAD database, including 34,573 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 0.67 (34573 hom., cov: 32)
• Consequence: LOC105378492 XR_946332.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.680

Genes affected

LOC105378492 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378492	XR_946332.1	n.306-737T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101483 AN: 151922 Hom.: 34560 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.668 AC: 101530 AN: 152040 Hom.: 34573 Cov.: 32 AF XY: 0.670 AC XY: 49834 AN XY: 74328

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.651

Alfa AF: 0.702 Hom.: 76176

Bravo AF: 0.670

Asia WGS AF: 0.768 AC: 2670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.9
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2782980; hg19: chr10-115781527;