rs2224536

Variant names:

• chr20-40027058-C-T
• rs2224536

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 0.499 in 152,070 control chromosomes in the GnomAD database, including 21,607 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 0.50 (21607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 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: 0.499 AC: 75899 AN: 151952 Hom.: 21606 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.499 AC: 75895 AN: 152070 Hom.: 21607 Cov.: 32 AF XY: 0.499 AC XY: 37090 AN XY: 74296

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.488

Alfa AF: 0.593 Hom.: 36624

Bravo AF: 0.480

Asia WGS AF: 0.508 AC: 1767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2224536; hg19: chr20-38655700;