9-11951222-C-A

Position:

• chr9-11951222-C-A

Variant summary

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

The ENST00000649122.1(ENSG00000285784):​n.388+23283C>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 0.0689 in 151,706 control chromosomes in the GnomAD database, including 695 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 0.069 (695 hom., cov: 32)
• Consequence: ENST00000649122.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.152 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.388+23283C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0687 AC: 10417 AN: 151588 Hom.: 691 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.0274

Gnomad FIN AF: 0.0344

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0268

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0689 AC: 10446 AN: 151706 Hom.: 695 Cov.: 32 AF XY: 0.0691 AC XY: 5123 AN XY: 74166

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0228

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.0272

Gnomad4 FIN AF: 0.0344

Gnomad4 NFE AF: 0.0268

Gnomad4 OTH AF: 0.0625

Alfa AF: 0.0321 Hom.: 200

Bravo AF: 0.0770

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1929412; hg19: chr9-11951222;