rs2405783

Positions:

• chr1-224838965-C-T

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, non coding transcript 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: ENST00000657178.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000657178.1	n.78-17977G>A		intron_variant, non_coding_transcript_variant

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;