rs803012

Variant names:

• chr14-52266005-A-G
• rs803012
• ENST00000835190.1:n.143+1431T>C

Variant summary

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

The ENST00000835190.1(ENSG00000308586):​n.143+1431T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,038 control chromosomes in the GnomAD database, including 2,589 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 0.18 (2589 hom., cov: 31)
• Consequence: ENSG00000308586 ENST00000835190.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107
• Publications: 7 publications found

Genes affected

ENSG00000308586 (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 = 0.214 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
ENSG00000308586	ENST00000835190.1	n.143+1431T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26733 AN: 151920 Hom.: 2594 Cov.: 31

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0872

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.176 AC: 26728 AN: 152038 Hom.: 2589 Cov.: 31 AF XY: 0.171 AC XY: 12692 AN XY: 74336

African (AFR) AF: 0.153 AC: 6342 AN: 41440

American (AMR) AF: 0.140 AC: 2135 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5184

South Asian (SAS) AF: 0.0860 AC: 415 AN: 4824

European-Finnish (FIN) AF: 0.181 AC: 1914 AN: 10568

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14734 AN: 67968

Other (OTH) AF: 0.196 AC: 411 AN: 2102

Alfa AF: 0.197 Hom.: 2064

Bravo AF: 0.173

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.41
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs803012; hg19: chr14-52732723;