9-22206988-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000435092.1(ENSG00000236921):n.374-2929G>A 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 0.443 in 152,018 control chromosomes in the GnomAD database, including 15,889 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 0.44 (15889 hom., cov: 32)
• Consequence: ENST00000435092.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.84

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435092.1	n.374-2929G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67312 AN: 151902 Hom.: 15899 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.443 AC: 67314 AN: 152018 Hom.: 15889 Cov.: 32 AF XY: 0.447 AC XY: 33246 AN XY: 74302

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.485

Alfa AF: 0.475 Hom.: 16209

Bravo AF: 0.438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
Cadd	Benign	20
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1679013; hg19: chr9-22206987;