rs1205091

Variant names:

• chr14-71812883-G-A
• rs1205091
• ENST00000787281.1:n.328+8165G>A

Variant summary

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

The ENST00000787281.1(ENSG00000302484):​n.328+8165G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,920 control chromosomes in the GnomAD database, including 14,362 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 0.43 (14362 hom., cov: 31)
• Consequence: ENSG00000302484 ENST00000787281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 1 publications found

Genes affected

ENSG00000302484 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.468 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
ENSG00000302484	ENST00000787281.1	n.328+8165G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65616 AN: 151802 Hom.: 14345 Cov.: 31

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.432 AC: 65681 AN: 151920 Hom.: 14362 Cov.: 31 AF XY: 0.432 AC XY: 32076 AN XY: 74242

African (AFR) AF: 0.408 AC: 16914 AN: 41448

American (AMR) AF: 0.477 AC: 7282 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3466

East Asian (EAS) AF: 0.369 AC: 1897 AN: 5136

South Asian (SAS) AF: 0.271 AC: 1304 AN: 4814

European-Finnish (FIN) AF: 0.490 AC: 5169 AN: 10546

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30936 AN: 67930

Other (OTH) AF: 0.399 AC: 842 AN: 2110

Alfa AF: 0.437 Hom.: 7737

Bravo AF: 0.433

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.52
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1205091; hg19: chr14-72279600;