13-26841536-A-T

Variant names:

• chr13-26841536-A-T
• rs9319321
• ENST00000767030.1:n.110-2579T>A

Variant summary

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

The ENST00000767030.1(ENSG00000299877):​n.110-2579T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,108 control chromosomes in the GnomAD database, including 44,406 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 0.76 (44406 hom., cov: 31)
• Consequence: ENSG00000299877 ENST00000767030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 14 publications found

Genes affected

ENSG00000299877 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767030.1. 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
	ENSG00000299877	ENST00000767030.1		n.110-2579T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115272 AN: 151990 Hom.: 44364 Cov.: 31

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.758 AC: 115361 AN: 152108 Hom.: 44406 Cov.: 31 AF XY: 0.746 AC XY: 55458 AN XY: 74340

African (AFR) AF: 0.874 AC: 36271 AN: 41510

American (AMR) AF: 0.650 AC: 9939 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2829 AN: 3464

East Asian (EAS) AF: 0.629 AC: 3254 AN: 5176

South Asian (SAS) AF: 0.622 AC: 2989 AN: 4804

European-Finnish (FIN) AF: 0.605 AC: 6379 AN: 10546

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51179 AN: 68002

Other (OTH) AF: 0.769 AC: 1622 AN: 2110

Alfa AF: 0.736 Hom.: 19907

Bravo AF: 0.766

Asia WGS AF: 0.608 AC: 2113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.014
DANN	Benign	0.68
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs9319321; hg19: chr13-27415673;