rs17135159

Positions:

• chr10-3366755-A-C

Variant summary

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

The NR_131187.1(LOC105376360):​n.162+47899A>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 0.212 in 152,100 control chromosomes in the GnomAD database, including 3,586 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 0.21 (3586 hom., cov: 32)
• Consequence: LOC105376360 NR_131187.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438

Genes affected

LOC105376360 (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 (EAS) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376360	NR_131187.1	n.162+47899A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32147 AN: 151980 Hom.: 3571 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.212 AC: 32180 AN: 152100 Hom.: 3586 Cov.: 32 AF XY: 0.219 AC XY: 16251 AN XY: 74332

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.236

Alfa AF: 0.190 Hom.: 414

Bravo AF: 0.213

Asia WGS AF: 0.293 AC: 1022 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	0.64
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17135159; hg19: chr10-3408947;