20-614136-T-C

Variant names:

• chr20-614136-T-C
• rs1533087

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 0.421 in 151,926 control chromosomes in the GnomAD database, including 14,817 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 0.42 (14817 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 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: 0.421 AC: 63868 AN: 151806 Hom.: 14802 Cov.: 30

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.421 AC: 63911 AN: 151926 Hom.: 14817 Cov.: 30 AF XY: 0.433 AC XY: 32164 AN XY: 74210

African (AFR) AF: 0.261 AC: 10821 AN: 41428

American (AMR) AF: 0.510 AC: 7780 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1441 AN: 3468

East Asian (EAS) AF: 0.842 AC: 4348 AN: 5164

South Asian (SAS) AF: 0.577 AC: 2767 AN: 4798

European-Finnish (FIN) AF: 0.544 AC: 5730 AN: 10524

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.436 AC: 29656 AN: 67968

Other (OTH) AF: 0.413 AC: 869 AN: 2106

Alfa AF: 0.421 Hom.: 14293

Bravo AF: 0.415

Asia WGS AF: 0.657 AC: 2284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.7
DANN	Benign	0.67
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1533087; hg19: chr20-594780;