rs1560382

Variant names:

• chr2-7339206-T-C
• rs1560382
• ENST00000812800.1:n.312+45073T>C

Variant summary

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

The ENST00000812800.1(ENSG00000229727):​n.312+45073T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,066 control chromosomes in the GnomAD database, including 25,443 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 0.57 (25443 hom., cov: 33)
• Consequence: ENSG00000229727 ENST00000812800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 2 publications found

Genes affected

ENSG00000229727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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
ENSG00000229727	ENST00000812800.1	n.312+45073T>C		intron_variant	Intron 1 of 5
ENSG00000229727	ENST00000812801.1	n.447-32923T>C		intron_variant	Intron 1 of 7
ENSG00000229727	ENST00000812802.1	n.447-32923T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86693 AN: 151948 Hom.: 25404 Cov.: 33

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.571 AC: 86790 AN: 152066 Hom.: 25443 Cov.: 33 AF XY: 0.571 AC XY: 42451 AN XY: 74362

African (AFR) AF: 0.644 AC: 26717 AN: 41456

American (AMR) AF: 0.636 AC: 9734 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1872 AN: 3468

East Asian (EAS) AF: 0.835 AC: 4324 AN: 5176

South Asian (SAS) AF: 0.547 AC: 2639 AN: 4826

European-Finnish (FIN) AF: 0.454 AC: 4785 AN: 10550

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.512 AC: 34833 AN: 67978

Other (OTH) AF: 0.581 AC: 1228 AN: 2114

Alfa AF: 0.507 Hom.: 6059

Bravo AF: 0.593

Asia WGS AF: 0.706 AC: 2454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.21
DANN	Benign	0.73
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1560382; hg19: chr2-7479337;