9-37579556-G-T

Variant names:

• chr9-37579556-G-T
• rs7042509
• ENST00000537239.2:n.*87+9255C>A

Variant summary

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

The ENST00000537239.2(ENSG00000256966):​n.*87+9255C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,094 control chromosomes in the GnomAD database, including 39,056 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 0.71 (39056 hom., cov: 32)
• Consequence: ENSG00000256966 ENST00000537239.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586
• Publications: 6 publications found

Genes affected

ENSG00000256966 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000537239.2. 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
	ENSG00000256966	ENST00000537239.2	TSL:5	n.*87+9255C>A		intron	N/A	ENSP00000457849.1	H3BUX3
	ENSG00000256966	ENST00000541804.1	TSL:1	n.62+9257C>A		intron	N/A
	ENSG00000256966	ENST00000544475.5	TSL:1	n.122+9197C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108295 AN: 151976 Hom.: 38990 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.713 AC: 108424 AN: 152094 Hom.: 39056 Cov.: 32 AF XY: 0.717 AC XY: 53293 AN XY: 74352

African (AFR) AF: 0.768 AC: 31877 AN: 41492

American (AMR) AF: 0.770 AC: 11764 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2131 AN: 3470

East Asian (EAS) AF: 0.940 AC: 4871 AN: 5184

South Asian (SAS) AF: 0.768 AC: 3706 AN: 4824

European-Finnish (FIN) AF: 0.669 AC: 7069 AN: 10574

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44618 AN: 67944

Other (OTH) AF: 0.708 AC: 1497 AN: 2114

Alfa AF: 0.672 Hom.: 24786

Bravo AF: 0.726

Asia WGS AF: 0.844 AC: 2934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.74
PhyloP100		-0.59
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7042509; hg19: chr9-37579553;