rs181654

Variant names:

• chr10-117620145-A-G
• rs181654
• ENST00000806653.1:n.92+9313A>G

Variant summary

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

The ENST00000806653.1(ENSG00000304858):​n.92+9313A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,876 control chromosomes in the GnomAD database, including 31,184 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 0.63 (31184 hom., cov: 31)
• Consequence: ENSG00000304858 ENST00000806653.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806653.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304858	ENST00000806653.1		n.92+9313A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95200 AN: 151758 Hom.: 31189 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.627 AC: 95203 AN: 151876 Hom.: 31184 Cov.: 31 AF XY: 0.624 AC XY: 46335 AN XY: 74224

African (AFR) AF: 0.438 AC: 18130 AN: 41380

American (AMR) AF: 0.605 AC: 9227 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2491 AN: 3470

East Asian (EAS) AF: 0.806 AC: 4155 AN: 5158

South Asian (SAS) AF: 0.771 AC: 3708 AN: 4812

European-Finnish (FIN) AF: 0.620 AC: 6533 AN: 10536

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48741 AN: 67958

Other (OTH) AF: 0.674 AC: 1421 AN: 2108

Alfa AF: 0.621 Hom.: 19143

Bravo AF: 0.617

Asia WGS AF: 0.705 AC: 2447 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.89
DANN	Benign	0.30
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs181654; hg19: chr10-119379656;