10-117619576-G-A

Variant names:

• chr10-117619576-G-A
• rs181652
• ENST00000806653.1:n.92+8744G>A

Variant summary

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

The ENST00000806653.1(ENSG00000304858):​n.92+8744G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,906 control chromosomes in the GnomAD database, including 19,221 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 0.49 (19221 hom., cov: 32)
• Consequence: ENSG00000304858 ENST00000806653.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 3 publications found

Genes affected

ENSG00000304858 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304858	ENST00000806653.1	n.92+8744G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75055 AN: 151788 Hom.: 19229 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.494 AC: 75042 AN: 151906 Hom.: 19221 Cov.: 32 AF XY: 0.497 AC XY: 36890 AN XY: 74222

African (AFR) AF: 0.359 AC: 14884 AN: 41406

American (AMR) AF: 0.470 AC: 7166 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2019 AN: 3470

East Asian (EAS) AF: 0.663 AC: 3422 AN: 5158

South Asian (SAS) AF: 0.622 AC: 2986 AN: 4802

European-Finnish (FIN) AF: 0.543 AC: 5728 AN: 10546

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36987 AN: 67966

Other (OTH) AF: 0.524 AC: 1102 AN: 2102

Alfa AF: 0.509 Hom.: 15536

Bravo AF: 0.482

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.1
DANN	Benign	0.42
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs181652; hg19: chr10-119379087;