13-30311086-A-G

Variant names:

• chr13-30311086-A-G
• rs185694
• ENST00000843926.1:n.219-7935A>G

Variant summary

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

The ENST00000843926.1(ENSG00000309792):​n.219-7935A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 144,828 control chromosomes in the GnomAD database, including 2,065 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 0.17 (2065 hom., cov: 33)
• Consequence: ENSG00000309792 ENST00000843926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 11 publications found

Genes affected

ENSG00000309792 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309792	ENST00000843926.1	n.219-7935A>G		intron_variant	Intron 2 of 2
ENSG00000309792	ENST00000843927.1	n.145+3743A>G		intron_variant	Intron 1 of 3
ENSG00000309792	ENST00000843928.1	n.199+3743A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.166 AC: 23995 AN: 144714 Hom.: 2064 Cov.: 33

Gnomad AFR AF: 0.0934

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.166 AC: 24003 AN: 144828 Hom.: 2065 Cov.: 33 AF XY: 0.171 AC XY: 12063 AN XY: 70418

African (AFR) AF: 0.0934 AC: 3493 AN: 37416

American (AMR) AF: 0.173 AC: 2468 AN: 14266

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 701 AN: 3410

East Asian (EAS) AF: 0.139 AC: 695 AN: 4994

South Asian (SAS) AF: 0.266 AC: 1208 AN: 4538

European-Finnish (FIN) AF: 0.275 AC: 2782 AN: 10132

Middle Eastern (MID) AF: 0.122 AC: 35 AN: 286

European-Non Finnish (NFE) AF: 0.182 AC: 12198 AN: 66882

Other (OTH) AF: 0.155 AC: 310 AN: 1998

Alfa AF: 0.165 Hom.: 3203

Bravo AF: 0.144

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.25
DANN	Benign	0.81
PhyloP100		0.073

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs185694; hg19: chr13-30885223;