9-11952979-G-A

Position:

• chr9-11952979-G-A

Variant summary

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

The ENST00000649122.1(ENSG00000285784):​n.388+25040G>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 0.0392 in 151,636 control chromosomes in the GnomAD database, including 172 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 0.039 (172 hom., cov: 32)
• Consequence: ENST00000649122.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.083 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+25040G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0392 AC: 5940 AN: 151516 Hom.: 172 Cov.: 32

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0269

Gnomad ASJ AF: 0.0370

Gnomad EAS AF: 0.0900

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.0476

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.0288

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

GnomAD4 genome AF: 0.0392 AC: 5937 AN: 151636 Hom.: 172 Cov.: 32 AF XY: 0.0384 AC XY: 2846 AN XY: 74128

Gnomad4 AFR AF: 0.0165

Gnomad4 AMR AF: 0.0269

Gnomad4 ASJ AF: 0.0370

Gnomad4 EAS AF: 0.0898

Gnomad4 SAS AF: 0.0110

Gnomad4 FIN AF: 0.0476

Gnomad4 NFE AF: 0.0527

Gnomad4 OTH AF: 0.0290

Alfa AF: 0.0428 Hom.: 32

Bravo AF: 0.0373

Asia WGS AF: 0.0440 AC: 153 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16928254; hg19: chr9-11952979;