10-117667447-A-G

Variant names:

• chr10-117667447-A-G
• rs855974
• ENST00000806653.1:n.93-8054A>G

Variant summary

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

The ENST00000806653.1(ENSG00000304858):​n.93-8054A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,956 control chromosomes in the GnomAD database, including 4,566 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 0.22 (4566 hom., cov: 32)
• Consequence: ENSG00000304858 ENST00000806653.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.624 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.93-8054A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33811 AN: 151838 Hom.: 4562 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.223 AC: 33824 AN: 151956 Hom.: 4566 Cov.: 32 AF XY: 0.227 AC XY: 16826 AN XY: 74224

African (AFR) AF: 0.108 AC: 4493 AN: 41458

American (AMR) AF: 0.282 AC: 4305 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3468

East Asian (EAS) AF: 0.642 AC: 3301 AN: 5140

South Asian (SAS) AF: 0.174 AC: 838 AN: 4812

European-Finnish (FIN) AF: 0.254 AC: 2690 AN: 10574

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16580 AN: 67926

Other (OTH) AF: 0.237 AC: 500 AN: 2108

Alfa AF: 0.243 Hom.: 15337

Bravo AF: 0.229

Asia WGS AF: 0.351 AC: 1221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.64
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs855974; hg19: chr10-119426958;