rs1427676

Variant names:

• chr2-203876443-C-T
• rs1427676

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.555 AC: 23016 AN: 41464

American (AMR) AF: 0.604 AC: 9236 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2533 AN: 3468

East Asian (EAS) AF: 0.406 AC: 2108 AN: 5186

South Asian (SAS) AF: 0.714 AC: 3438 AN: 4816

European-Finnish (FIN) AF: 0.497 AC: 5244 AN: 10552

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45100 AN: 67982

Other (OTH) AF: 0.664 AC: 1402 AN: 2110

Alfa AF: 0.647 Hom.: 19158

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
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1427676; hg19: chr2-204741166;