rs2220327

Variant names:

• chr13-64372566-T-C
• rs2220327

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 0.43 in 151,960 control chromosomes in the GnomAD database, including 14,431 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 0.43 (14431 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.512 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: 0.429 AC: 65199 AN: 151842 Hom.: 14405 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.430 AC: 65279 AN: 151960 Hom.: 14431 Cov.: 32 AF XY: 0.425 AC XY: 31555 AN XY: 74282

African (AFR) AF: 0.413 AC: 17126 AN: 41424

American (AMR) AF: 0.521 AC: 7958 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1427 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1216 AN: 5156

South Asian (SAS) AF: 0.391 AC: 1887 AN: 4826

European-Finnish (FIN) AF: 0.307 AC: 3243 AN: 10572

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30912 AN: 67930

Other (OTH) AF: 0.435 AC: 919 AN: 2112

Alfa AF: 0.461 Hom.: 2878

Bravo AF: 0.445

Asia WGS AF: 0.371 AC: 1289 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	1.1
DANN	Benign	0.40
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2220327; hg19: chr13-64946698;