rs9321063

Variant names:

• chr6-98448791-A-G
• rs9321063
• ENST00000847792.1:n.648-1891A>G

Variant summary

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

The ENST00000847792.1(ENSG00000271860):​n.648-1891A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0695 in 152,172 control chromosomes in the GnomAD database, including 413 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 0.069 (413 hom., cov: 33)
• Consequence: ENSG00000271860 ENST00000847792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456
• Publications: 4 publications found

Genes affected

ENSG00000271860 (HGNC:58964):

ENSG00000310228 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0993 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000847792.1. 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
	ENSG00000271860	ENST00000847792.1		n.648-1891A>G		intron	N/A
	ENSG00000271860	ENST00000847793.1		n.612-1891A>G		intron	N/A
	ENSG00000271860	ENST00000847794.1		n.461-13532A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0694 AC: 10548 AN: 152054 Hom.: 412 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0753

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.00737

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0599

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0695 AC: 10569 AN: 152172 Hom.: 413 Cov.: 33 AF XY: 0.0705 AC XY: 5243 AN XY: 74372

African (AFR) AF: 0.102 AC: 4232 AN: 41548

American (AMR) AF: 0.0752 AC: 1149 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3472

East Asian (EAS) AF: 0.00719 AC: 37 AN: 5146

South Asian (SAS) AF: 0.0112 AC: 54 AN: 4822

European-Finnish (FIN) AF: 0.0753 AC: 799 AN: 10606

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.0599 AC: 4073 AN: 67988

Other (OTH) AF: 0.0601 AC: 127 AN: 2112

Alfa AF: 0.0599 Hom.: 530

Bravo AF: 0.0717

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.62
DANN	Benign	0.17
PhyloP100		-0.46

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: rs9321063;

hg19: chr6-98896667;