10-8180249-G-A

Position:

• chr10-8180249-G-A

Variant summary

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

The XR_001747361.2(LOC107984206):​n.196+1255C>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 0.0792 in 151,902 control chromosomes in the GnomAD database, including 614 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 0.079 (614 hom., cov: 32)
• Consequence: LOC107984206 XR_001747361.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892

Genes affected

LOC107984206 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984206	XR_001747361.2	n.196+1255C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0792 AC: 12019 AN: 151784 Hom.: 615 Cov.: 32

Gnomad AFR AF: 0.0214

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0895

Gnomad ASJ AF: 0.0852

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0792 AC: 12025 AN: 151902 Hom.: 614 Cov.: 32 AF XY: 0.0815 AC XY: 6052 AN XY: 74266

Gnomad4 AFR AF: 0.0214

Gnomad4 AMR AF: 0.0896

Gnomad4 ASJ AF: 0.0852

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0799

Alfa AF: 0.0992 Hom.: 386

Bravo AF: 0.0722

Asia WGS AF: 0.0460 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.38
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508344; hg19: chr10-8222212;