chr9-27623560-G-A

Variant names:

• chr9-27623560-G-A
• rs3913107
• ENST00000827310.1:n.697-37174C>T

Variant summary

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

The ENST00000827310.1(ENSG00000307594):​n.697-37174C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 151,980 control chromosomes in the GnomAD database, including 59,780 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 0.89 (59780 hom., cov: 31)
• Consequence: ENSG00000307594 ENST00000827310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307594	ENST00000827310.1		n.697-37174C>T		intron	N/A
	ENSG00000307594	ENST00000827311.1		n.389-37174C>T		intron	N/A
	ENSG00000307594	ENST00000827312.1		n.741-37174C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134558 AN: 151862 Hom.: 59757 Cov.: 31

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.886 AC: 134629 AN: 151980 Hom.: 59780 Cov.: 31 AF XY: 0.886 AC XY: 65803 AN XY: 74302

African (AFR) AF: 0.847 AC: 35029 AN: 41336

American (AMR) AF: 0.877 AC: 13401 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.923 AC: 3206 AN: 3472

East Asian (EAS) AF: 0.983 AC: 5105 AN: 5192

South Asian (SAS) AF: 0.927 AC: 4470 AN: 4820

European-Finnish (FIN) AF: 0.866 AC: 9161 AN: 10580

Middle Eastern (MID) AF: 0.925 AC: 270 AN: 292

European-Non Finnish (NFE) AF: 0.901 AC: 61252 AN: 67986

Other (OTH) AF: 0.889 AC: 1872 AN: 2106

Alfa AF: 0.895 Hom.: 110774

Bravo AF: 0.884

Asia WGS AF: 0.908 AC: 3134 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.6
DANN	Benign	0.34
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs3913107; hg19: chr9-27623558;