chr9-35996556-C-T

Variant names:

• chr9-35996556-C-T
• rs12006109
• ENST00000647905.1:n.273-16481C>T

Variant summary

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

The ENST00000647905.1(ENSG00000290538):​n.273-16481C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 152,204 control chromosomes in the GnomAD database, including 441 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 0.058 (441 hom., cov: 32)
• Consequence: ENSG00000290538 ENST00000647905.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 1 publications found

Genes affected

ENSG00000290538 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 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
ENSG00000290538	ENST00000647905.1	n.273-16481C>T		intron_variant	Intron 2 of 2
ENSG00000290538	ENST00000806593.1	n.57-16481C>T		intron_variant	Intron 1 of 1
ENSG00000290538	ENST00000806594.1	n.330-16481C>T		intron_variant	Intron 1 of 1
ENSG00000290538	ENST00000806595.1	n.298-16381C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0577 AC: 8781 AN: 152086 Hom.: 439 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0330

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.00576

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0348

Gnomad OTH AF: 0.0556

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

GnomAD4 genome AF: 0.0578 AC: 8803 AN: 152204 Hom.: 441 Cov.: 32 AF XY: 0.0556 AC XY: 4135 AN XY: 74428

African (AFR) AF: 0.135 AC: 5592 AN: 41504

American (AMR) AF: 0.0330 AC: 504 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0212 AC: 102 AN: 4818

European-Finnish (FIN) AF: 0.00576 AC: 61 AN: 10598

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0348 AC: 2368 AN: 68028

Other (OTH) AF: 0.0550 AC: 116 AN: 2110

Alfa AF: 0.0468 Hom.: 111

Bravo AF: 0.0637

Asia WGS AF: 0.0250 AC: 86 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.61
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs12006109; hg19: chr9-35996553;