rs10786808

Variant names:

• chr10-104624857-T-C
• rs10786808
• ENST00000649412.1:n.*62T>C

Variant summary

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

The ENST00000649412.1(ENSG00000237761):​n.*62T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 151,770 control chromosomes in the GnomAD database, including 48,245 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 0.80 (48245 hom., cov: 32)
• Consequence: ENSG00000237761 ENST00000649412.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 0 publications found

Genes affected

ENSG00000237761 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378464	XR_007062285.1	n.*65T>C		downstream_gene_variant
LOC105378464	XR_946282.2	n.*87T>C		downstream_gene_variant
LOC105378464	XR_946283.1	n.*114T>C		downstream_gene_variant
LOC105378464	XR_946284.1	n.*114T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237761	ENST00000649412.1	n.*62T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.796 AC: 120721 AN: 151652 Hom.: 48225 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.796 AC: 120784 AN: 151770 Hom.: 48245 Cov.: 32 AF XY: 0.797 AC XY: 59121 AN XY: 74178

African (AFR) AF: 0.765 AC: 31652 AN: 41392

American (AMR) AF: 0.747 AC: 11388 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2856 AN: 3466

East Asian (EAS) AF: 0.779 AC: 4019 AN: 5156

South Asian (SAS) AF: 0.661 AC: 3196 AN: 4832

European-Finnish (FIN) AF: 0.892 AC: 9366 AN: 10498

Middle Eastern (MID) AF: 0.791 AC: 231 AN: 292

European-Non Finnish (NFE) AF: 0.819 AC: 55578 AN: 67868

Other (OTH) AF: 0.800 AC: 1685 AN: 2106

Alfa AF: 0.796 Hom.: 31590

Bravo AF: 0.789

Asia WGS AF: 0.672 AC: 2336 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.37
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10786808; hg19: chr10-106384615;