20-33273180-C-T

Variant names:

• chr20-33273180-C-T
• rs6057807

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 0.0621 in 152,116 control chromosomes in the GnomAD database, including 317 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 0.062 (317 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0883 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: 0.0620 AC: 9425 AN: 151998 Hom.: 316 Cov.: 32

Gnomad AFR AF: 0.0904

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0371

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.0361

Gnomad SAS AF: 0.0330

Gnomad FIN AF: 0.0508

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0575

Gnomad OTH AF: 0.0560

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

GnomAD4 genome AF: 0.0621 AC: 9446 AN: 152116 Hom.: 317 Cov.: 32 AF XY: 0.0603 AC XY: 4481 AN XY: 74364

African (AFR) AF: 0.0907 AC: 3763 AN: 41498

American (AMR) AF: 0.0370 AC: 566 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3468

East Asian (EAS) AF: 0.0360 AC: 186 AN: 5162

South Asian (SAS) AF: 0.0330 AC: 159 AN: 4816

European-Finnish (FIN) AF: 0.0508 AC: 538 AN: 10590

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0575 AC: 3909 AN: 67982

Other (OTH) AF: 0.0569 AC: 120 AN: 2110

Alfa AF: 0.0584 Hom.: 45

Bravo AF: 0.0611

Asia WGS AF: 0.0560 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.2
DANN	Benign	0.95
PhyloP100		-0.16
PromoterAI		-0.0018	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6057807; hg19: chr20-31860986;