chr13-74678686-C-A

Variant names:

• chr13-74678686-C-A
• rs1854204
• ENST00000814867.1:n.125-29085G>T

Variant summary

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

The ENST00000814867.1(ENSG00000306024):​n.125-29085G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,190 control chromosomes in the GnomAD database, including 1,536 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 0.14 (1536 hom., cov: 32)
• Consequence: ENSG00000306024 ENST00000814867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814867.1. 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
	ENSG00000306024	ENST00000814867.1		n.125-29085G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20669 AN: 152072 Hom.: 1535 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.0891

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.0508

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.136 AC: 20680 AN: 152190 Hom.: 1536 Cov.: 32 AF XY: 0.134 AC XY: 9986 AN XY: 74422

African (AFR) AF: 0.169 AC: 7028 AN: 41516

American (AMR) AF: 0.0888 AC: 1357 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0914 AC: 317 AN: 3470

East Asian (EAS) AF: 0.0509 AC: 264 AN: 5186

South Asian (SAS) AF: 0.154 AC: 744 AN: 4824

European-Finnish (FIN) AF: 0.111 AC: 1180 AN: 10616

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9340 AN: 67982

Other (OTH) AF: 0.124 AC: 261 AN: 2112

Alfa AF: 0.125 Hom.: 2277

Bravo AF: 0.134

Asia WGS AF: 0.114 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.074
DANN	Benign	0.24
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1854204; hg19: chr13-75252823;