chr10-22809163-T-C

Variant names:

• chr10-22809163-T-C
• rs11013140
• ENST00000756997.1:n.127-2261A>G

Variant summary

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

The ENST00000756997.1(ENSG00000298626):​n.127-2261A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,086 control chromosomes in the GnomAD database, including 14,349 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 0.41 (14349 hom., cov: 32)
• Consequence: ENSG00000298626 ENST00000756997.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 4 publications found

Genes affected

ENSG00000298626 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756997.1. 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
	ENSG00000298626	ENST00000756997.1		n.127-2261A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61873 AN: 151968 Hom.: 14322 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.407 AC: 61956 AN: 152086 Hom.: 14349 Cov.: 32 AF XY: 0.401 AC XY: 29796 AN XY: 74342

African (AFR) AF: 0.641 AC: 26568 AN: 41446

American (AMR) AF: 0.385 AC: 5884 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 959 AN: 3470

East Asian (EAS) AF: 0.556 AC: 2878 AN: 5172

South Asian (SAS) AF: 0.376 AC: 1811 AN: 4812

European-Finnish (FIN) AF: 0.190 AC: 2008 AN: 10596

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20616 AN: 67994

Other (OTH) AF: 0.400 AC: 847 AN: 2116

Alfa AF: 0.295 Hom.: 1856

Bravo AF: 0.432

Asia WGS AF: 0.441 AC: 1533 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	0.99
DANN	Benign	0.22
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs11013140; hg19: chr10-23098092;