chr9-37576451-T-G

Position:

• chr9-37576451-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000537239.2(ENSG00000256966):​n.*87+12360A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,214 control chromosomes in the GnomAD database, including 45,385 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 0.77 (45369 hom., cov: 33)
  • Exomes 𝑓: 0.72 (16 hom.)
• Consequence: ENSG00000256966 ENST00000537239.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110

Genes affected

ENSG00000256966 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37576451T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000256966	ENST00000537239.2	n.*87+12360A>C		intron_variant		5		ENSP00000457849.1
ENSG00000256966	ENST00000541804.1	n.62+12362A>C		intron_variant		1
ENSG00000256966	ENST00000544475.5	n.122+12302A>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117107 AN: 152036 Hom.: 45304 Cov.: 33

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.762

GnomAD4 exome AF: 0.717 AC: 43 AN: 60 Hom.: 16 AF XY: 0.675 AC XY: 27 AN XY: 40

Gnomad4 ASJ exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.800

Gnomad4 NFE exome AF: 0.750

GnomAD4 genome AF: 0.770 AC: 117232 AN: 152154 Hom.: 45369 Cov.: 33 AF XY: 0.774 AC XY: 57586 AN XY: 74390

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.815

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.947

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.734

Gnomad4 OTH AF: 0.765

Alfa AF: 0.754 Hom.: 6489

Bravo AF: 0.780

Asia WGS AF: 0.903 AC: 3141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.7
DANN	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs6476643; hg19: chr9-37576448;