chr9-27664164-C-T

Variant names:

• chr9-27664164-C-T
• rs10511813
• ENST00000827310.1:n.696+20080G>A

Variant summary

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

The ENST00000827310.1(ENSG00000307594):​n.696+20080G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,072 control chromosomes in the GnomAD database, including 2,413 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 0.16 (2413 hom., cov: 30)
• Consequence: ENSG00000307594 ENST00000827310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530
• Publications: 4 publications found

Genes affected

ENSG00000307594 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376002	XR_007061441.1	n.-203C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307594	ENST00000827310.1	n.696+20080G>A		intron_variant	Intron 3 of 3
ENSG00000307594	ENST00000827311.1	n.388+26355G>A		intron_variant	Intron 1 of 1
ENSG00000307594	ENST00000827312.1	n.740+20080G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24026 AN: 151954 Hom.: 2410 Cov.: 30

Gnomad AFR AF: 0.0544

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.0388

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.158 AC: 24031 AN: 152072 Hom.: 2413 Cov.: 30 AF XY: 0.156 AC XY: 11576 AN XY: 74328

African (AFR) AF: 0.0542 AC: 2249 AN: 41480

American (AMR) AF: 0.178 AC: 2718 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3468

East Asian (EAS) AF: 0.0387 AC: 200 AN: 5172

South Asian (SAS) AF: 0.155 AC: 747 AN: 4818

European-Finnish (FIN) AF: 0.156 AC: 1650 AN: 10582

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14718 AN: 67966

Other (OTH) AF: 0.202 AC: 428 AN: 2114

Alfa AF: 0.198 Hom.: 10453

Bravo AF: 0.157

Asia WGS AF: 0.124 AC: 431 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	0.29
DANN	Benign	0.51
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs10511813; hg19: chr9-27664162;