13-90718206-C-T

Variant names:

• chr13-90718206-C-T
• rs828200
• ENST00000741265.1:n.292+2698G>A

Variant summary

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

The ENST00000741265.1(ENSG00000296712):​n.292+2698G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.964 in 152,142 control chromosomes in the GnomAD database, including 70,913 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 0.96 (70913 hom., cov: 33)
• Consequence: ENSG00000296712 ENST00000741265.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723
• Publications: 2 publications found

Genes affected

ENSG00000296712 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741265.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296712	ENST00000741265.1		n.292+2698G>A		intron	N/A
	ENSG00000296744	ENST00000741517.1		n.356-338C>T		intron	N/A
	ENSG00000296744	ENST00000741518.1		n.542-338C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.964 AC: 146535 AN: 152024 Hom.: 70857 Cov.: 33

Gnomad AFR AF: 0.874

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.987

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.994

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.968

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

GnomAD4 genome AF: 0.964 AC: 146648 AN: 152142 Hom.: 70913 Cov.: 33 AF XY: 0.966 AC XY: 71819 AN XY: 74374

African (AFR) AF: 0.875 AC: 36306 AN: 41508

American (AMR) AF: 0.987 AC: 15047 AN: 15252

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3468 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5176 AN: 5176

South Asian (SAS) AF: 1.00 AC: 4828 AN: 4828

European-Finnish (FIN) AF: 1.00 AC: 10628 AN: 10628

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 67948 AN: 67966

Other (OTH) AF: 0.968 AC: 2043 AN: 2110

Alfa AF: 0.975 Hom.: 10331

Bravo AF: 0.959

Asia WGS AF: 0.996 AC: 3465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.88
DANN	Benign	0.18
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs828200; hg19: chr13-91370460;