ENST00000841361.1:n.233-587G>A

Variant names:

• chr14-73231840-G-A
• rs362408
• ENST00000841361.1:n.233-587G>A

Variant summary

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

The ENST00000841361.1(ENSG00000309481):​n.233-587G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0903 in 152,252 control chromosomes in the GnomAD database, including 732 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 0.090 (732 hom., cov: 32)
• Consequence: ENSG00000309481 ENST00000841361.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 4 publications found

Genes affected

ENSG00000309481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 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
ENSG00000309481	ENST00000841361.1	n.233-587G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0905 AC: 13762 AN: 152134 Hom.: 736 Cov.: 32

Gnomad AFR AF: 0.0522

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0684

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.0903 AC: 13754 AN: 152252 Hom.: 732 Cov.: 32 AF XY: 0.0889 AC XY: 6615 AN XY: 74442

African (AFR) AF: 0.0521 AC: 2166 AN: 41550

American (AMR) AF: 0.108 AC: 1655 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 435 AN: 3470

East Asian (EAS) AF: 0.194 AC: 1005 AN: 5182

South Asian (SAS) AF: 0.0650 AC: 314 AN: 4828

European-Finnish (FIN) AF: 0.0684 AC: 726 AN: 10612

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7041 AN: 67998

Other (OTH) AF: 0.127 AC: 268 AN: 2114

Alfa AF: 0.0993 Hom.: 374

Bravo AF: 0.0933

Asia WGS AF: 0.131 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.20
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs362408; hg19: chr14-73698548;