13-104367011-C-A

Variant names:

• chr13-104367011-C-A
• rs714668
• ENST00000844365.1:n.199+538C>A

Variant summary

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

The ENST00000844365.1(ENSG00000309849):​n.199+538C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,028 control chromosomes in the GnomAD database, including 3,953 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 0.22 (3953 hom., cov: 32)
• Consequence: ENSG00000309849 ENST00000844365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 1 publications found

Genes affected

ENSG00000309849 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 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
ENSG00000309849	ENST00000844365.1	n.199+538C>A		intron_variant	Intron 2 of 2
ENSG00000309849	ENST00000844366.1	n.105-1110C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33302 AN: 151910 Hom.: 3947 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.219 AC: 33341 AN: 152028 Hom.: 3953 Cov.: 32 AF XY: 0.223 AC XY: 16567 AN XY: 74294

African (AFR) AF: 0.229 AC: 9484 AN: 41504

American (AMR) AF: 0.238 AC: 3636 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 349 AN: 3466

East Asian (EAS) AF: 0.377 AC: 1937 AN: 5144

South Asian (SAS) AF: 0.182 AC: 881 AN: 4828

European-Finnish (FIN) AF: 0.272 AC: 2865 AN: 10540

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13663 AN: 67972

Other (OTH) AF: 0.198 AC: 418 AN: 2110

Alfa AF: 0.186 Hom.: 1222

Bravo AF: 0.219

Asia WGS AF: 0.306 AC: 1063 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.76
DANN	Benign	0.36
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs714668; hg19: chr13-105019361;