rs9398652

Variant names:

• chr6-121824888-C-A
• rs9398652
• ENST00000780084.1:n.193-33023C>A

Variant summary

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

The ENST00000780084.1(ENSG00000289871):​n.193-33023C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,880 control chromosomes in the GnomAD database, including 6,505 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 0.23 (6505 hom., cov: 32)
• Consequence: ENSG00000289871 ENST00000780084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 21 publications found

Genes affected

ENSG00000289871 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780084.1. 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
	ENSG00000289871	ENST00000780084.1		n.193-33023C>A		intron	N/A
	ENSG00000289871	ENST00000780085.1		n.80-33023C>A		intron	N/A
	ENSG00000289871	ENST00000780086.1		n.109-40965C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34499 AN: 151760 Hom.: 6472 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0976

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.0999

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.228 AC: 34580 AN: 151880 Hom.: 6505 Cov.: 32 AF XY: 0.226 AC XY: 16802 AN XY: 74224

African (AFR) AF: 0.504 AC: 20886 AN: 41424

American (AMR) AF: 0.121 AC: 1850 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0976 AC: 338 AN: 3462

East Asian (EAS) AF: 0.452 AC: 2318 AN: 5128

South Asian (SAS) AF: 0.108 AC: 522 AN: 4828

European-Finnish (FIN) AF: 0.132 AC: 1396 AN: 10580

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.0998 AC: 6780 AN: 67906

Other (OTH) AF: 0.202 AC: 427 AN: 2110

Alfa AF: 0.148 Hom.: 8126

Bravo AF: 0.241

Asia WGS AF: 0.304 AC: 1052 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.11
PhyloP100		-0.12

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: rs9398652;

hg19: chr6-122146034;