rs10840002

Variant names:

• chr11-8221479-A-G
• rs10840002
• ENST00000825479.1:n.229-2225A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-8221479-A-G
• chr11-8221479-A-T

Variant summary

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

The ENST00000825479.1(ENSG00000307368):​n.229-2225A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,966 control chromosomes in the GnomAD database, including 21,186 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 0.50 (21186 hom., cov: 31)
• Consequence: ENSG00000307368 ENST00000825479.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651
• Publications: 19 publications found

Genes affected

ENSG00000307368 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000825479.1. 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
	ENSG00000307368	ENST00000825479.1		n.229-2225A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75434 AN: 151848 Hom.: 21189 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.496 AC: 75446 AN: 151966 Hom.: 21186 Cov.: 31 AF XY: 0.497 AC XY: 36882 AN XY: 74262

African (AFR) AF: 0.214 AC: 8888 AN: 41454

American (AMR) AF: 0.584 AC: 8930 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1933 AN: 3468

East Asian (EAS) AF: 0.438 AC: 2253 AN: 5148

South Asian (SAS) AF: 0.521 AC: 2512 AN: 4822

European-Finnish (FIN) AF: 0.585 AC: 6170 AN: 10556

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42944 AN: 67918

Other (OTH) AF: 0.513 AC: 1084 AN: 2112

Alfa AF: 0.591 Hom.: 46710

Bravo AF: 0.484

Asia WGS AF: 0.447 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.61
PhyloP100		0.65

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10840002;

hg19: chr11-8243026;