9-27616916-A-G

Variant names:

• chr9-27616916-A-G
• rs10511814
• ENST00000827310.1:n.697-30530T>C

Variant summary

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

The ENST00000827310.1(ENSG00000307594):​n.697-30530T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0173 in 152,338 control chromosomes in the GnomAD database, including 59 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 0.017 (59 hom., cov: 33)
• Consequence: ENSG00000307594 ENST00000827310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.0799 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827310.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307594	ENST00000827310.1		n.697-30530T>C		intron	N/A
	ENSG00000307594	ENST00000827311.1		n.389-30530T>C		intron	N/A
	ENSG00000307594	ENST00000827312.1		n.741-30530T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0173 AC: 2627 AN: 152220 Hom.: 58 Cov.: 33

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.0869

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.00245

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00585

Gnomad OTH AF: 0.0129

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

GnomAD4 genome AF: 0.0173 AC: 2634 AN: 152338 Hom.: 59 Cov.: 33 AF XY: 0.0175 AC XY: 1302 AN XY: 74506

African (AFR) AF: 0.0248 AC: 1033 AN: 41578

American (AMR) AF: 0.0393 AC: 602 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3470

East Asian (EAS) AF: 0.0865 AC: 449 AN: 5188

South Asian (SAS) AF: 0.0164 AC: 79 AN: 4822

European-Finnish (FIN) AF: 0.00245 AC: 26 AN: 10622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00585 AC: 398 AN: 68032

Other (OTH) AF: 0.0142 AC: 30 AN: 2114

Alfa AF: 0.0203 Hom.: 16

Bravo AF: 0.0225

Asia WGS AF: 0.0480 AC: 168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs10511814; hg19: chr9-27616914;