17-70142903-T-C

Variant names:

• chr17-70142903-T-C
• rs9896573
• ENST00000756635.1:n.426-4470A>G

Variant summary

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

The ENST00000756635.1(ENSG00000298578):​n.426-4470A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,290 control chromosomes in the GnomAD database, including 951 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 0.11 (951 hom., cov: 32)
• Consequence: ENSG00000298578 ENST00000756635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 4 publications found

Genes affected

ENSG00000298578 (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 = 0.17 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756635.1. 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
	ENSG00000298578	ENST00000756635.1		n.426-4470A>G		intron	N/A
	ENSG00000298578	ENST00000756636.1		n.414-3439A>G		intron	N/A
	ENSG00000298578	ENST00000756637.1		n.504-3439A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17261 AN: 152172 Hom.: 949 Cov.: 32

Gnomad AFR AF: 0.0860

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0958

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.113 AC: 17275 AN: 152290 Hom.: 951 Cov.: 32 AF XY: 0.114 AC XY: 8505 AN XY: 74468

African (AFR) AF: 0.0859 AC: 3568 AN: 41552

American (AMR) AF: 0.175 AC: 2686 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 443 AN: 3468

East Asian (EAS) AF: 0.101 AC: 523 AN: 5182

South Asian (SAS) AF: 0.169 AC: 816 AN: 4830

European-Finnish (FIN) AF: 0.0958 AC: 1017 AN: 10614

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7845 AN: 68020

Other (OTH) AF: 0.118 AC: 249 AN: 2112

Alfa AF: 0.0773 Hom.: 111

Bravo AF: 0.118

Asia WGS AF: 0.121 AC: 419 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	0.34
DANN	Benign	0.71
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs9896573; hg19: chr17-68139044;