rs9300810

Variant names:

• chr13-103355807-C-G
• rs9300810
• ENST00000648788.1:n.55+12093C>G

Your query was ambiguous. Multiple possible variants found:

• chr13-103355807-C-G
• chr13-103355807-C-T

Variant summary

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

The ENST00000648788.1(ENSG00000285789):​n.55+12093C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,196 control chromosomes in the GnomAD database, including 1,927 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 0.15 (1927 hom., cov: 32)
• Consequence: ENSG00000285789 ENST00000648788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537
• Publications: 3 publications found

Genes affected

ENSG00000285789 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648788.1. 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
	ENSG00000285789	ENST00000648788.1		n.55+12093C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23215 AN: 152078 Hom.: 1927 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.153 AC: 23233 AN: 152196 Hom.: 1927 Cov.: 32 AF XY: 0.149 AC XY: 11110 AN XY: 74426

African (AFR) AF: 0.176 AC: 7293 AN: 41508

American (AMR) AF: 0.0956 AC: 1463 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3472

East Asian (EAS) AF: 0.0282 AC: 146 AN: 5184

South Asian (SAS) AF: 0.120 AC: 579 AN: 4826

European-Finnish (FIN) AF: 0.153 AC: 1615 AN: 10586

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11354 AN: 68004

Other (OTH) AF: 0.129 AC: 273 AN: 2110

Alfa AF: 0.0861 Hom.: 125

Bravo AF: 0.149

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.081
DANN	Benign	0.39
PhyloP100		-0.54

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: rs9300810;

hg19: chr13-104008157;