chr9-69951820-T-C

Variant names:

• chr9-69951820-T-C
• rs1389119
• ENST00000721035.1:n.222+12915T>C

Variant summary

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

The ENST00000721035.1(ENSG00000294102):​n.222+12915T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,986 control chromosomes in the GnomAD database, including 21,280 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 0.52 (21280 hom., cov: 32)
• Consequence: ENSG00000294102 ENST00000721035.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 2 publications found

Genes affected

ENSG00000294102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 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
ENSG00000294102	ENST00000721035.1	n.222+12915T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79359 AN: 151868 Hom.: 21254 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.523 AC: 79429 AN: 151986 Hom.: 21280 Cov.: 32 AF XY: 0.519 AC XY: 38536 AN XY: 74298

African (AFR) AF: 0.621 AC: 25751 AN: 41446

American (AMR) AF: 0.457 AC: 6964 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1974 AN: 3470

East Asian (EAS) AF: 0.160 AC: 825 AN: 5170

South Asian (SAS) AF: 0.468 AC: 2254 AN: 4814

European-Finnish (FIN) AF: 0.549 AC: 5803 AN: 10574

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34262 AN: 67954

Other (OTH) AF: 0.506 AC: 1067 AN: 2110

Alfa AF: 0.503 Hom.: 26563

Bravo AF: 0.514

Asia WGS AF: 0.342 AC: 1187 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.80
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1389119; hg19: chr9-72566736;