rs1365786

Variant names:

• chr2-125643184-T-A
• rs1365786
• ENST00000794704.1:n.215+114A>T

Variant summary

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

The ENST00000794704.1(ENSG00000303452):​n.215+114A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,018 control chromosomes in the GnomAD database, including 12,152 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 0.40 (12152 hom., cov: 32)
• Consequence: ENSG00000303452 ENST00000794704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.30
• Publications: 0 publications found

Genes affected

ENSG00000303452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.441 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
ENSG00000303452	ENST00000794704.1	n.215+114A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60152 AN: 151898 Hom.: 12144 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.396 AC: 60187 AN: 152018 Hom.: 12152 Cov.: 32 AF XY: 0.389 AC XY: 28873 AN XY: 74316

African (AFR) AF: 0.344 AC: 14267 AN: 41466

American (AMR) AF: 0.449 AC: 6867 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1441 AN: 3470

East Asian (EAS) AF: 0.191 AC: 984 AN: 5152

South Asian (SAS) AF: 0.298 AC: 1436 AN: 4824

European-Finnish (FIN) AF: 0.371 AC: 3925 AN: 10570

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30046 AN: 67940

Other (OTH) AF: 0.388 AC: 820 AN: 2114

Alfa AF: 0.426 Hom.: 1725

Bravo AF: 0.400

Asia WGS AF: 0.243 AC: 845 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.85
DANN	Benign	0.38
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs1365786; hg19: chr2-126400761;