chr9-13007130-T-C

Position:

• chr9-13007130-T-C

Variant summary

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

The ENST00000649120.1(ENSG00000285637):​n.326-1826A>G 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 0.898 in 152,236 control chromosomes in the GnomAD database, including 61,672 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 0.90 (61672 hom., cov: 32)
• Consequence: ENST00000649120.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.935 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
	ENST00000649120.1	n.326-1826A>G		intron_variant, non_coding_transcript_variant
	ENST00000666564.1	n.326-1826A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.898 AC: 136626 AN: 152118 Hom.: 61647 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.960

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.898 AC: 136697 AN: 152236 Hom.: 61672 Cov.: 32 AF XY: 0.896 AC XY: 66717 AN XY: 74440

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.929

Gnomad4 ASJ AF: 0.967

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.975

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.888

Alfa AF: 0.930 Hom.: 142418

Bravo AF: 0.895

Asia WGS AF: 0.807 AC: 2809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1360517; hg19: chr9-13007129;