9-120099019-T-C

Variant names:

• chr9-120099019-T-C
• rs16909449
• ENST00000840715.1:n.335-14705A>G

Variant summary

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

The ENST00000840715.1(ENSG00000309396):​n.335-14705A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,182 control chromosomes in the GnomAD database, including 2,866 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 0.18 (2866 hom., cov: 32)
• Consequence: ENSG00000309396 ENST00000840715.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.669
• Publications: 6 publications found

Genes affected

ENSG00000309396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 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
ENSG00000309396	ENST00000840715.1	n.335-14705A>G		intron_variant	Intron 2 of 4
ENSG00000309396	ENST00000840716.1	n.245-14705A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27164 AN: 152062 Hom.: 2867 Cov.: 32

Gnomad AFR AF: 0.0646

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.179 AC: 27169 AN: 152182 Hom.: 2866 Cov.: 32 AF XY: 0.179 AC XY: 13317 AN XY: 74388

African (AFR) AF: 0.0645 AC: 2682 AN: 41550

American (AMR) AF: 0.196 AC: 3001 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 501 AN: 3472

East Asian (EAS) AF: 0.399 AC: 2061 AN: 5168

South Asian (SAS) AF: 0.153 AC: 740 AN: 4824

European-Finnish (FIN) AF: 0.237 AC: 2508 AN: 10580

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15121 AN: 67982

Other (OTH) AF: 0.173 AC: 364 AN: 2110

Alfa AF: 0.199 Hom.: 7238

Bravo AF: 0.171

Asia WGS AF: 0.271 AC: 940 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.5
DANN	Benign	0.58
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs16909449; hg19: chr9-122861297;