10-8591898-C-T

Position:

• chr10-8591898-C-T

Variant summary

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

The NR_134492.1(LOC105376398):​n.44+2450G>A 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 0.328 in 151,866 control chromosomes in the GnomAD database, including 8,937 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 0.33 (8937 hom., cov: 32)
• Consequence: LOC105376398 NR_134492.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

LOC105376398 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376398	NR_134492.1	n.44+2450G>A		intron_variant, non_coding_transcript_variant
LOC105376399	XR_001747362.2	n.162+26C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49674 AN: 151748 Hom.: 8907 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.328 AC: 49760 AN: 151866 Hom.: 8937 Cov.: 32 AF XY: 0.329 AC XY: 24401 AN XY: 74210

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.312

Alfa AF: 0.271 Hom.: 6446

Bravo AF: 0.342

Asia WGS AF: 0.484 AC: 1680 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.057
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4749791; hg19: chr10-8633861;