rs10795668

Variant names:

• chr10-8659256-G-A
• rs10795668
• ENST00000750870.1:n.102-40C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000750870.1(ENSG00000297769):​n.102-40C>T variant causes a intron 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: ENSG00000297769 ENST00000750870.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 165 publications found

Genes affected

ENSG00000297769 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105376400	XR_001747277.2	n.99-40C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297769	ENST00000750870.1	n.102-40C>T		intron_variant	Intron 1 of 1
ENSG00000297769	ENST00000750865.1	n.-38C>T		upstream_gene_variant
ENSG00000297769	ENST00000750866.1	n.-40C>T		upstream_gene_variant

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

African (AFR) AF: 0.0605 AC: 2513 AN: 41526

American (AMR) AF: 0.311 AC: 4750 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1059 AN: 3470

East Asian (EAS) AF: 0.369 AC: 1901 AN: 5158

South Asian (SAS) AF: 0.248 AC: 1193 AN: 4818

European-Finnish (FIN) AF: 0.292 AC: 3083 AN: 10562

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21848 AN: 67982

Other (OTH) AF: 0.277 AC: 586 AN: 2112

Alfa AF: 0.301 Hom.: 33530

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10795668; hg19: chr10-8701219;