rs4467276

Variant names:

• chr2-126080627-C-T
• rs4467276

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 0.257 in 151,948 control chromosomes in the GnomAD database, including 5,162 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 (5162 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 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: 0.257 AC: 38990 AN: 151834 Hom.: 5161 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.257 AC: 39009 AN: 151948 Hom.: 5162 Cov.: 32 AF XY: 0.257 AC XY: 19106 AN XY: 74232

African (AFR) AF: 0.264 AC: 10939 AN: 41454

American (AMR) AF: 0.235 AC: 3589 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3472

East Asian (EAS) AF: 0.138 AC: 710 AN: 5140

South Asian (SAS) AF: 0.223 AC: 1073 AN: 4816

European-Finnish (FIN) AF: 0.315 AC: 3323 AN: 10550

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.264 AC: 17924 AN: 67966

Other (OTH) AF: 0.255 AC: 536 AN: 2104

Alfa AF: 0.269 Hom.: 729

Bravo AF: 0.252

Asia WGS AF: 0.176 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.83
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs4467276; hg19: chr2-126838204;