20-3452511-C-T

Variant names:

• chr20-3452511-C-T
• rs979332

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 0.506 in 152,070 control chromosomes in the GnomAD database, including 20,113 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 0.51 (20113 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 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: 0.506 AC: 76941 AN: 151952 Hom.: 20093 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.506 AC: 76997 AN: 152070 Hom.: 20113 Cov.: 32 AF XY: 0.504 AC XY: 37498 AN XY: 74328

African (AFR) AF: 0.633 AC: 26282 AN: 41492

American (AMR) AF: 0.427 AC: 6517 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1655 AN: 3470

East Asian (EAS) AF: 0.341 AC: 1763 AN: 5172

South Asian (SAS) AF: 0.370 AC: 1785 AN: 4826

European-Finnish (FIN) AF: 0.531 AC: 5615 AN: 10568

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.469 AC: 31862 AN: 67962

Other (OTH) AF: 0.491 AC: 1035 AN: 2106

Alfa AF: 0.474 Hom.: 71605

Bravo AF: 0.502

Asia WGS AF: 0.335 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.6
DANN	Benign	0.66
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs979332; hg19: chr20-3433158;