rs10761866

Positions:

• chr10-64815798-T-C

Variant summary

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

The XR_946020.2(LOC105378336):​n.49+796T>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 0.195 in 151,994 control chromosomes in the GnomAD database, including 3,039 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 (3039 hom., cov: 32)
• Consequence: LOC105378336 XR_946020.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587

Genes affected

LOC105378336 (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 (SAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378336	XR_946020.2	n.49+796T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29580 AN: 151876 Hom.: 3039 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.195 AC: 29589 AN: 151994 Hom.: 3039 Cov.: 32 AF XY: 0.200 AC XY: 14836 AN XY: 74270

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.196

Alfa AF: 0.199 Hom.: 676

Bravo AF: 0.179

Asia WGS AF: 0.223 AC: 771 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10761866; hg19: chr10-66575555;