chr9-12028131-G-T

Position:

• chr9-12028131-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649122.1(ENSG00000285784):​n.389-28084G>T variant causes a intron, non coding transcript 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: ENST00000649122.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000649122.1	n.389-28084G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.345

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

Splicing

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

Publications

LitVar

Other links and lift over

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