13-105596960-T-C

Variant names:

• chr13-105596960-T-C
• rs1549059
• ENST00000831788.1:n.697-23613A>G

Variant summary

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

The ENST00000831788.1(ENSG00000308108):​n.697-23613A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 151,946 control chromosomes in the GnomAD database, including 27,917 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 0.60 (27917 hom., cov: 32)
• Consequence: ENSG00000308108 ENST00000831788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611
• Publications: 4 publications found

Genes affected

ENSG00000308108 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000831788.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308108	ENST00000831788.1		n.697-23613A>G		intron	N/A
	ENSG00000289454	ENST00000688787.2		n.*243A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91846 AN: 151828 Hom.: 27900 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.605 AC: 91923 AN: 151946 Hom.: 27917 Cov.: 32 AF XY: 0.601 AC XY: 44648 AN XY: 74278

African (AFR) AF: 0.580 AC: 24021 AN: 41436

American (AMR) AF: 0.550 AC: 8382 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2139 AN: 3472

East Asian (EAS) AF: 0.566 AC: 2923 AN: 5166

South Asian (SAS) AF: 0.589 AC: 2839 AN: 4816

European-Finnish (FIN) AF: 0.617 AC: 6517 AN: 10560

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43286 AN: 67924

Other (OTH) AF: 0.552 AC: 1167 AN: 2114

Alfa AF: 0.620 Hom.: 81813

Bravo AF: 0.599

Asia WGS AF: 0.608 AC: 2112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.66
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs1549059; hg19: chr13-106249309;