rs2320597

Variant names:

• chr13-21959469-C-A
• rs2320597
• ENST00000808243.1:n.188-9099C>A

Variant summary

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

The ENST00000808243.1(ENSG00000305062):​n.188-9099C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0486 in 152,122 control chromosomes in the GnomAD database, including 512 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 0.049 (512 hom., cov: 32)
• Consequence: ENSG00000305062 ENST00000808243.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867
• Publications: 2 publications found

Genes affected

ENSG00000305062 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808243.1. 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
	ENSG00000305062	ENST00000808243.1		n.188-9099C>A		intron	N/A
	ENSG00000305062	ENST00000808244.1		n.300-9099C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0484 AC: 7356 AN: 152006 Hom.: 507 Cov.: 32

Gnomad AFR AF: 0.0762

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.0796

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00981

Gnomad OTH AF: 0.0387

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

GnomAD4 genome AF: 0.0486 AC: 7390 AN: 152122 Hom.: 512 Cov.: 32 AF XY: 0.0525 AC XY: 3901 AN XY: 74374

African (AFR) AF: 0.0767 AC: 3180 AN: 41486

American (AMR) AF: 0.0750 AC: 1147 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3470

East Asian (EAS) AF: 0.339 AC: 1752 AN: 5170

South Asian (SAS) AF: 0.0799 AC: 384 AN: 4806

European-Finnish (FIN) AF: 0.0103 AC: 109 AN: 10582

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00981 AC: 667 AN: 68000

Other (OTH) AF: 0.0402 AC: 85 AN: 2114

Alfa AF: 0.0226 Hom.: 461

Bravo AF: 0.0557

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.042
DANN	Benign	0.37
PhyloP100		-0.87

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: rs2320597;

hg19: chr13-22533608;