rs10508262

chr10-3709082-C-G

Variant summary

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

The NR_131187.1(LOC105376360):n.163-39606C>G 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 0.193 in 152,052 control chromosomes in the GnomAD database, including 3,229 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 0.19 (3229 hom., cov: 32)
• Consequence: LOC105376360 NR_131187.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

Genes affected

LOC105376360 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376360	NR_131187.1	n.163-39606C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29378 AN: 151934 Hom.: 3229 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.193 AC: 29376 AN: 152052 Hom.: 3229 Cov.: 32 AF XY: 0.195 AC XY: 14480 AN XY: 74318

Gnomad4 AFR AF: 0.0874

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.196

Alfa AF: 0.228 Hom.: 569

Bravo AF: 0.182

Asia WGS AF: 0.201 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.6
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508262; hg19: chr10-3751274;