rs11008099

Variant names:

• chr10-30545703-G-A
• rs11008099
• ENST00000670247.2:n.327-8251G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-30545703-G-A
• chr10-30545703-G-T

Variant summary

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

The ENST00000670247.2(ENSG00000287420):​n.327-8251G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0758 in 152,028 control chromosomes in the GnomAD database, including 596 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 0.076 (596 hom., cov: 31)
• Consequence: ENSG00000287420 ENST00000670247.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 4 publications found

Genes affected

ENSG00000287420 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670247.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287420	ENST00000670247.2		n.327-8251G>A		intron	N/A
	ENSG00000287420	ENST00000844209.1		n.289-8179G>A		intron	N/A
	ENSG00000287420	ENST00000844210.1		n.191-8283G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0758 AC: 11519 AN: 151910 Hom.: 594 Cov.: 31

Gnomad AFR AF: 0.0409

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0601

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0525

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0857

Gnomad OTH AF: 0.0845

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

GnomAD4 genome AF: 0.0758 AC: 11527 AN: 152028 Hom.: 596 Cov.: 31 AF XY: 0.0750 AC XY: 5575 AN XY: 74322

African (AFR) AF: 0.0410 AC: 1701 AN: 41486

American (AMR) AF: 0.0600 AC: 915 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0718 AC: 249 AN: 3466

East Asian (EAS) AF: 0.243 AC: 1257 AN: 5176

South Asian (SAS) AF: 0.148 AC: 710 AN: 4800

European-Finnish (FIN) AF: 0.0525 AC: 555 AN: 10580

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0858 AC: 5828 AN: 67962

Other (OTH) AF: 0.0860 AC: 181 AN: 2104

Alfa AF: 0.0772 Hom.: 880

Bravo AF: 0.0737

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.51
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11008099; hg19: chr10-30834632;