13-74701583-C-T

Variant names:

• chr13-74701583-C-T
• rs2077779
• ENST00000814867.1:n.124+31117G>A

Variant summary

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

The ENST00000814867.1(ENSG00000306024):​n.124+31117G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 152,020 control chromosomes in the GnomAD database, including 27,521 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 (27521 hom., cov: 31)
• Consequence: ENSG00000306024 ENST00000814867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648
• Publications: 6 publications found

Genes affected

ENSG00000306024 (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 (EAS) allele frequency at 95% confidence interval = 0.787 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
ENSG00000306024	ENST00000814867.1	n.124+31117G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90866 AN: 151904 Hom.: 27509 Cov.: 31

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.598 AC: 90911 AN: 152020 Hom.: 27521 Cov.: 31 AF XY: 0.601 AC XY: 44648 AN XY: 74306

African (AFR) AF: 0.566 AC: 23476 AN: 41454

American (AMR) AF: 0.629 AC: 9609 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2395 AN: 3468

East Asian (EAS) AF: 0.808 AC: 4166 AN: 5158

South Asian (SAS) AF: 0.733 AC: 3534 AN: 4824

European-Finnish (FIN) AF: 0.596 AC: 6290 AN: 10562

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39284 AN: 67950

Other (OTH) AF: 0.657 AC: 1388 AN: 2112

Alfa AF: 0.592 Hom.: 14919

Bravo AF: 0.604

Asia WGS AF: 0.745 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.64
DANN	Benign	0.74
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs2077779; hg19: chr13-75275720;