rs2405783

Variant names:

• chr1-224838965-C-T
• rs2405783
• ENST00000657178.1:n.78-17977G>A

Variant summary

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

The ENST00000657178.1(ENSG00000286719):​n.78-17977G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,912 control chromosomes in the GnomAD database, including 20,218 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 0.51 (20218 hom., cov: 31)
• Consequence: ENSG00000286719 ENST00000657178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810

Genes affected

ENSG00000286719 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 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
ENSG00000286719	ENST00000657178.1	n.78-17977G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77122 AN: 151794 Hom.: 20198 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.508 AC: 77185 AN: 151912 Hom.: 20218 Cov.: 31 AF XY: 0.503 AC XY: 37371 AN XY: 74240

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.509

Alfa AF: 0.513 Hom.: 3641

Bravo AF: 0.498

Asia WGS AF: 0.292 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2405783; hg19: chr1-225026667;