ENST00000729186.1:n.223-2121T>C

Variant names:

• chr9-134222034-A-G
• rs11185668
• ENST00000729186.1:n.223-2121T>C

Variant summary

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

The ENST00000729186.1(ENSG00000295308):​n.223-2121T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 151,996 control chromosomes in the GnomAD database, including 38,105 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 0.70 (38105 hom., cov: 31)
• Consequence: ENSG00000295308 ENST00000729186.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 4 publications found

Genes affected

ENSG00000295308 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 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
ENSG00000295308	ENST00000729186.1	n.223-2121T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106313 AN: 151878 Hom.: 38051 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.700 AC: 106431 AN: 151996 Hom.: 38105 Cov.: 31 AF XY: 0.703 AC XY: 52235 AN XY: 74284

African (AFR) AF: 0.824 AC: 34155 AN: 41454

American (AMR) AF: 0.758 AC: 11577 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 2834 AN: 3472

East Asian (EAS) AF: 0.815 AC: 4195 AN: 5150

South Asian (SAS) AF: 0.745 AC: 3586 AN: 4812

European-Finnish (FIN) AF: 0.619 AC: 6530 AN: 10552

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41114 AN: 67966

Other (OTH) AF: 0.744 AC: 1569 AN: 2110

Alfa AF: 0.652 Hom.: 50578

Bravo AF: 0.717

Asia WGS AF: 0.808 AC: 2811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.83
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs11185668; hg19: chr9-137113880; COSMIC: COSV61535178;