rs2220327

Variant names:

• chr13-64372566-T-C
• rs2220327

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 0.43 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.429 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

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.435

Alfa AF: 0.463 Hom.: 2809

Bravo AF: 0.445

Asia WGS AF: 0.371 AC: 1289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2220327; hg19: chr13-64946698;