rs2409780

Variant names:

• chr8-11480078-T-C
• rs2409780
• ENST00000644741.1:n.273+275A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000644741.1(ENSG00000284957):​n.273+275A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,136 control chromosomes in the GnomAD database, including 6,494 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 0.26 (6494 hom., cov: 32)
• Consequence: ENSG00000284957 ENST00000644741.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

ENSG00000284957 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 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
ENSG00000284957	ENST00000644741.1	n.273+275A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39367 AN: 152018 Hom.: 6477 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.259 AC: 39398 AN: 152136 Hom.: 6494 Cov.: 32 AF XY: 0.267 AC XY: 19826 AN XY: 74368

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.265

Alfa AF: 0.240 Hom.: 588

Bravo AF: 0.273

Asia WGS AF: 0.545 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2409780; hg19: chr8-11337587;