10-113297684-A-G

Variant names:

• chr10-113297684-A-G
• rs11196288
• ENST00000818152.1:n.269+34171A>G

Variant summary

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

The ENST00000818152.1(ENSG00000306410):​n.269+34171A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0594 in 152,226 control chromosomes in the GnomAD database, including 554 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 0.059 (554 hom., cov: 31)
• Consequence: ENSG00000306410 ENST00000818152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 11 publications found

Genes affected

ENSG00000306410 (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 (EAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818152.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306410	ENST00000818152.1		n.269+34171A>G		intron	N/A
	ENSG00000306410	ENST00000818153.1		n.124+34285A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0593 AC: 9019 AN: 152108 Hom.: 544 Cov.: 31

Gnomad AFR AF: 0.0617

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0717

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0361

Gnomad OTH AF: 0.0517

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

GnomAD4 genome AF: 0.0594 AC: 9035 AN: 152226 Hom.: 554 Cov.: 31 AF XY: 0.0612 AC XY: 4553 AN XY: 74434

African (AFR) AF: 0.0616 AC: 2559 AN: 41542

American (AMR) AF: 0.0716 AC: 1095 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3468

East Asian (EAS) AF: 0.353 AC: 1824 AN: 5164

South Asian (SAS) AF: 0.102 AC: 490 AN: 4806

European-Finnish (FIN) AF: 0.0352 AC: 374 AN: 10620

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0361 AC: 2457 AN: 68010

Other (OTH) AF: 0.0606 AC: 128 AN: 2112

Alfa AF: 0.0414 Hom.: 27

Bravo AF: 0.0633

Asia WGS AF: 0.262 AC: 907 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	0.88
DANN	Benign	0.77
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs11196288; hg19: chr10-115057443;