rs2409780

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

Genes affected

ENSG00000284957 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644741.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284957	ENST00000644741.1		n.273+275A>G		intron	N/A

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

African (AFR) AF: 0.138 AC: 5727 AN: 41522

American (AMR) AF: 0.444 AC: 6786 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3468

East Asian (EAS) AF: 0.721 AC: 3727 AN: 5166

South Asian (SAS) AF: 0.358 AC: 1727 AN: 4822

European-Finnish (FIN) AF: 0.273 AC: 2891 AN: 10582

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17253 AN: 67974

Other (OTH) AF: 0.265 AC: 561 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.30
PhyloP100		0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2409780;

hg19: chr8-11337587;