9-13009676-G-C

Position:

• chr9-13009676-G-C

Variant summary

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

The ENST00000649120.1(ENSG00000285637):​n.326-4372C>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 0.81 in 152,120 control chromosomes in the GnomAD database, including 51,930 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 0.81 (51930 hom., cov: 32)
• Consequence: ENST00000649120.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 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.326-4372C>G		intron_variant, non_coding_transcript_variant
	ENST00000666564.1	n.326-4372C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.810 AC: 123125 AN: 152002 Hom.: 51921 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.810 AC: 123163 AN: 152120 Hom.: 51930 Cov.: 32 AF XY: 0.810 AC XY: 60299 AN XY: 74404

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.962

Gnomad4 NFE AF: 0.926

Gnomad4 OTH AF: 0.821

Alfa AF: 0.869 Hom.: 6919

Bravo AF: 0.794

Asia WGS AF: 0.772 AC: 2686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.71
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1412307; hg19: chr9-13009675;