9-13007130-T-C

Variant names:

• chr9-13007130-T-C
• rs1360517
• ENST00000649120.1:n.326-1826A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649120.1(ENSG00000285637):​n.326-1826A>G variant causes a intron 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: ENSG00000285637 ENST00000649120.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268
• Publications: 11 publications found

Genes affected

ENSG00000285637 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285637	ENST00000649120.1	n.326-1826A>G		intron_variant	Intron 2 of 5
ENSG00000285637	ENST00000666564.1	n.326-1826A>G		intron_variant	Intron 2 of 4
ENSG00000285637	ENST00000826321.1	n.713-1826A>G		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.809 AC: 33612 AN: 41526

American (AMR) AF: 0.929 AC: 14193 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3356 AN: 3470

East Asian (EAS) AF: 0.871 AC: 4507 AN: 5172

South Asian (SAS) AF: 0.758 AC: 3652 AN: 4816

European-Finnish (FIN) AF: 0.975 AC: 10349 AN: 10616

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 64025 AN: 68036

Other (OTH) AF: 0.888 AC: 1877 AN: 2114

Alfa AF: 0.925 Hom.: 280663

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
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1360517; hg19: chr9-13007129;