9-12028131-G-T

Variant names:

• chr9-12028131-G-T
• rs1374172
• ENST00000649122.1:n.389-28084G>T

Variant summary

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

The ENST00000649122.1(ENSG00000285784):​n.389-28084G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,454 control chromosomes in the GnomAD database, including 10,316 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 0.34 (10316 hom., cov: 32)
• Consequence: ENSG00000285784 ENST00000649122.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241
• Publications: 2 publications found

Genes affected

ENSG00000285784 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.459 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
ENSG00000285784	ENST00000649122.1	n.389-28084G>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50807 AN: 151332 Hom.: 10318 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.335 AC: 50809 AN: 151454 Hom.: 10316 Cov.: 32 AF XY: 0.334 AC XY: 24703 AN XY: 74004

African (AFR) AF: 0.120 AC: 4963 AN: 41328

American (AMR) AF: 0.277 AC: 4206 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1371 AN: 3456

East Asian (EAS) AF: 0.309 AC: 1583 AN: 5124

South Asian (SAS) AF: 0.471 AC: 2260 AN: 4802

European-Finnish (FIN) AF: 0.374 AC: 3937 AN: 10532

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31369 AN: 67748

Other (OTH) AF: 0.345 AC: 724 AN: 2096

Alfa AF: 0.258 Hom.: 712

Bravo AF: 0.313

Asia WGS AF: 0.342 AC: 1180 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.6
DANN	Benign	0.44
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1374172; hg19: chr9-12028131; COSMIC: COSV69447747;