chr9-73550478-T-C

Variant names:

• chr9-73550478-T-C
• rs368408
• ENST00000715871.1:n.182-27391T>C

Variant summary

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

The ENST00000715871.1(ENSG00000232590):​n.182-27391T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 151,856 control chromosomes in the GnomAD database, including 55,566 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 0.84 (55566 hom., cov: 31)
• Consequence: ENSG00000232590 ENST00000715871.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 3 publications found

Genes affected

ENSG00000232590 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715871.1. 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
	ENSG00000232590	ENST00000715871.1		n.182-27391T>C		intron	N/A
	ENSG00000232590	ENST00000715872.1		n.196-52886T>C		intron	N/A
	ENSG00000232590	ENST00000715873.1		n.120-92707T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128028 AN: 151742 Hom.: 55547 Cov.: 31

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.844 AC: 128097 AN: 151856 Hom.: 55566 Cov.: 31 AF XY: 0.843 AC XY: 62563 AN XY: 74206

African (AFR) AF: 0.622 AC: 25741 AN: 41384

American (AMR) AF: 0.875 AC: 13335 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3141 AN: 3464

East Asian (EAS) AF: 0.778 AC: 4018 AN: 5164

South Asian (SAS) AF: 0.875 AC: 4214 AN: 4814

European-Finnish (FIN) AF: 0.921 AC: 9745 AN: 10586

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.956 AC: 64918 AN: 67882

Other (OTH) AF: 0.869 AC: 1836 AN: 2112

Alfa AF: 0.885 Hom.: 10577

Bravo AF: 0.828

Asia WGS AF: 0.811 AC: 2811 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.63
DANN	Benign	0.46
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs368408; hg19: chr9-76165394;