9-37579556-G-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000256966 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256966	ENST00000537239.2	n.*87+9255C>A		intron_variant	Intron 2 of 2	5		ENSP00000457849.1
ENSG00000256966	ENST00000541804.1	n.62+9257C>A		intron_variant	Intron 1 of 8	1
ENSG00000256966	ENST00000544475.5	n.122+9197C>A		intron_variant	Intron 1 of 10	1

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

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.940

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.708

Alfa AF: 0.672 Hom.: 18089

Bravo AF: 0.726

Asia WGS AF: 0.844 AC: 2934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.74

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

Publications

LitVar

Other links and lift over

dbSNP: rs7042509; hg19: chr9-37579553;