9-115440437-T-C

Variant names:

• chr9-115440437-T-C
• rs9409154
• ENST00000646338.1:n.276-115003A>G

Variant summary

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

The ENST00000646338.1(ENSG00000228714):​n.276-115003A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,128 control chromosomes in the GnomAD database, including 4,161 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 0.21 (4161 hom., cov: 33)
• Consequence: ENSG00000228714 ENST00000646338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454
• Publications: 5 publications found

Genes affected

ENSG00000228714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 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
ENSG00000228714	ENST00000646338.1	n.276-115003A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31525 AN: 152010 Hom.: 4148 Cov.: 33

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.208 AC: 31581 AN: 152128 Hom.: 4161 Cov.: 33 AF XY: 0.211 AC XY: 15674 AN XY: 74370

African (AFR) AF: 0.358 AC: 14844 AN: 41478

American (AMR) AF: 0.163 AC: 2488 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3472

East Asian (EAS) AF: 0.401 AC: 2068 AN: 5162

South Asian (SAS) AF: 0.156 AC: 753 AN: 4828

European-Finnish (FIN) AF: 0.210 AC: 2222 AN: 10598

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8323 AN: 68000

Other (OTH) AF: 0.181 AC: 384 AN: 2116

Alfa AF: 0.158 Hom.: 4510

Bravo AF: 0.211

Asia WGS AF: 0.294 AC: 1020 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.65
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs9409154; hg19: chr9-118202716;