2-16941470-A-C

Variant names:

• chr2-16941470-A-C
• rs4832481

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 0.25 in 152,016 control chromosomes in the GnomAD database, including 6,140 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 0.25 (6140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37851 AN: 151898 Hom.: 6122 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.250 AC: 37932 AN: 152016 Hom.: 6140 Cov.: 32 AF XY: 0.256 AC XY: 19060 AN XY: 74326

African (AFR) AF: 0.373 AC: 15446 AN: 41452

American (AMR) AF: 0.351 AC: 5353 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 619 AN: 3466

East Asian (EAS) AF: 0.640 AC: 3298 AN: 5156

South Asian (SAS) AF: 0.246 AC: 1185 AN: 4808

European-Finnish (FIN) AF: 0.178 AC: 1886 AN: 10594

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9446 AN: 67960

Other (OTH) AF: 0.242 AC: 511 AN: 2112

Alfa AF: 0.169 Hom.: 1389

Bravo AF: 0.275

Asia WGS AF: 0.441 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.62
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs4832481; hg19: chr2-17122737;