rs1427676

chr2-203876443-C-T

Variant summary

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

The variant allele was found at a frequency of 0.611 in 152,064 control chromosomes in the GnomAD database, including 28,879 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 0.61 (28879 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92814 AN: 151946 Hom.: 28867 Cov.: 33

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.611 AC: 92872 AN: 152064 Hom.: 28879 Cov.: 33 AF XY: 0.604 AC XY: 44879 AN XY: 74332

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.664

Alfa AF: 0.646 Hom.: 16696

Bravo AF: 0.612

Asia WGS AF: 0.602 AC: 2096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	6.8
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1427676; hg19: chr2-204741166;