13-31416382-A-G

Variant names:

• chr13-31416382-A-G
• rs11841788
• ENST00000843719.1:n.219+4881A>G

Variant summary

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

The ENST00000843719.1(ENSG00000278305):​n.219+4881A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,072 control chromosomes in the GnomAD database, including 5,132 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 0.23 (5132 hom., cov: 32)
• Consequence: ENSG00000278305 ENST00000843719.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63
• Publications: 2 publications found

Genes affected

ENSG00000278305 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843719.1. 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
	ENSG00000278305	ENST00000843719.1		n.219+4881A>G		intron	N/A
	ENSG00000278305	ENST00000843720.1		n.336+4881A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35518 AN: 151956 Hom.: 5119 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.234 AC: 35567 AN: 152072 Hom.: 5132 Cov.: 32 AF XY: 0.240 AC XY: 17857 AN XY: 74328

African (AFR) AF: 0.350 AC: 14506 AN: 41454

American (AMR) AF: 0.230 AC: 3511 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3472

East Asian (EAS) AF: 0.574 AC: 2956 AN: 5146

South Asian (SAS) AF: 0.348 AC: 1673 AN: 4810

European-Finnish (FIN) AF: 0.200 AC: 2118 AN: 10580

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9823 AN: 68006

Other (OTH) AF: 0.207 AC: 437 AN: 2114

Alfa AF: 0.166 Hom.: 4418

Bravo AF: 0.240

Asia WGS AF: 0.445 AC: 1544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0030
DANN	Benign	0.27
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs11841788; hg19: chr13-31990519;