rs9363864

Variant names:

• chr6-68182664-G-A
• rs9363864
• ENST00000718116.1:n.418-40005G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000718116.1(ENSG00000285838):​n.418-40005G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,864 control chromosomes in the GnomAD database, including 11,110 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 0.35 (11110 hom., cov: 32)
• Consequence: ENSG00000285838 ENST00000718116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 5 publications found

Genes affected

ENSG00000285838 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718116.1. 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
	ENSG00000285838	ENST00000718116.1		n.418-40005G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53118 AN: 151746 Hom.: 11108 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.350 AC: 53121 AN: 151864 Hom.: 11110 Cov.: 32 AF XY: 0.352 AC XY: 26121 AN XY: 74192

African (AFR) AF: 0.103 AC: 4253 AN: 41446

American (AMR) AF: 0.406 AC: 6183 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3466

East Asian (EAS) AF: 0.532 AC: 2730 AN: 5132

South Asian (SAS) AF: 0.329 AC: 1583 AN: 4812

European-Finnish (FIN) AF: 0.430 AC: 4542 AN: 10556

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.455 AC: 30901 AN: 67912

Other (OTH) AF: 0.396 AC: 834 AN: 2104

Alfa AF: 0.424 Hom.: 7252

Bravo AF: 0.343

Asia WGS AF: 0.385 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	14
DANN	Benign	0.80
PhyloP100		1.1

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: rs9363864;

hg19: chr6-68892556;