9-73542784-G-A

Variant names:

• chr9-73542784-G-A
• rs12555078
• ENST00000667966.1:n.269+5279C>T

Variant summary

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

The ENST00000667966.1(ENSG00000286840):​n.269+5279C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0783 in 151,980 control chromosomes in the GnomAD database, including 532 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 0.078 (532 hom., cov: 32)
• Consequence: ENSG00000286840 ENST00000667966.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 7 publications found

Genes affected

ENSG00000286840 (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 (AMR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667966.1. 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
	ENSG00000286840	ENST00000667966.1		n.269+5279C>T		intron	N/A
	ENSG00000232590	ENST00000715871.1		n.182-35085G>A		intron	N/A
	ENSG00000232590	ENST00000715872.1		n.196-60580G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0783 AC: 11891 AN: 151862 Hom.: 532 Cov.: 32

Gnomad AFR AF: 0.0879

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0459

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.0563

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.0705

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

GnomAD4 genome AF: 0.0783 AC: 11894 AN: 151980 Hom.: 532 Cov.: 32 AF XY: 0.0778 AC XY: 5782 AN XY: 74274

African (AFR) AF: 0.0878 AC: 3640 AN: 41436

American (AMR) AF: 0.119 AC: 1817 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0459 AC: 159 AN: 3464

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5160

South Asian (SAS) AF: 0.0482 AC: 232 AN: 4818

European-Finnish (FIN) AF: 0.0563 AC: 595 AN: 10568

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0765 AC: 5201 AN: 67970

Other (OTH) AF: 0.0697 AC: 147 AN: 2108

Alfa AF: 0.0756 Hom.: 519

Bravo AF: 0.0807

Asia WGS AF: 0.0300 AC: 105 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	2.2
DANN	Benign	0.54
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs12555078; hg19: chr9-76157700;