rs10795668

Positions:

• chr10-8659256-G-A

Variant summary

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

The XR_001747277.2(LOC105376400):​n.99-40C>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 0.246 in 152,092 control chromosomes in the GnomAD database, including 5,644 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 0.25 (5644 hom., cov: 32)
• Consequence: LOC105376400 XR_001747277.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

LOC105376400 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376400	XR_001747277.2	n.99-40C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37314 AN: 151976 Hom.: 5627 Cov.: 32

Gnomad AFR AF: 0.0607

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.246 AC: 37340 AN: 152092 Hom.: 5644 Cov.: 32 AF XY: 0.247 AC XY: 18331 AN XY: 74332

Gnomad4 AFR AF: 0.0605

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.277

Alfa AF: 0.309 Hom.: 16705

Bravo AF: 0.239

Asia WGS AF: 0.299 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10795668; hg19: chr10-8701219;