rs9788982

Variant names:

• chr17-70143644-A-G
• rs9788982
• ENST00000756635.1:n.426-5211T>C

Variant summary

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

The ENST00000756635.1(ENSG00000298578):​n.426-5211T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,064 control chromosomes in the GnomAD database, including 1,157 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 0.12 (1157 hom., cov: 32)
• Consequence: ENSG00000298578 ENST00000756635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.178 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

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
	ENSG00000298578	ENST00000756635.1		n.426-5211T>C		intron	N/A
	ENSG00000298578	ENST00000756636.1		n.414-4180T>C		intron	N/A
	ENSG00000298578	ENST00000756637.1		n.504-4180T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18890 AN: 151946 Hom.: 1155 Cov.: 32

Gnomad AFR AF: 0.0888

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.124 AC: 18902 AN: 152064 Hom.: 1157 Cov.: 32 AF XY: 0.125 AC XY: 9258 AN XY: 74342

African (AFR) AF: 0.0886 AC: 3677 AN: 41484

American (AMR) AF: 0.183 AC: 2801 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3462

East Asian (EAS) AF: 0.101 AC: 522 AN: 5172

South Asian (SAS) AF: 0.175 AC: 842 AN: 4818

European-Finnish (FIN) AF: 0.107 AC: 1132 AN: 10574

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9022 AN: 67978

Other (OTH) AF: 0.126 AC: 265 AN: 2104

Alfa AF: 0.123 Hom.: 140

Bravo AF: 0.128

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.75
DANN	Benign	0.22
PhyloP100		-0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9788982;

hg19: chr17-68139785;