chr20-60710120-C-T

Variant names:

• chr20-60710120-C-T
• rs2144880

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 0.307 in 151,794 control chromosomes in the GnomAD database, including 8,464 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 0.31 (8464 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.789
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 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: 0.307 AC: 46632 AN: 151692 Hom.: 8458 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.307 AC: 46661 AN: 151794 Hom.: 8464 Cov.: 32 AF XY: 0.307 AC XY: 22788 AN XY: 74186

African (AFR) AF: 0.124 AC: 5110 AN: 41366

American (AMR) AF: 0.343 AC: 5233 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3466

East Asian (EAS) AF: 0.168 AC: 870 AN: 5178

South Asian (SAS) AF: 0.362 AC: 1744 AN: 4814

European-Finnish (FIN) AF: 0.355 AC: 3723 AN: 10474

Middle Eastern (MID) AF: 0.362 AC: 105 AN: 290

European-Non Finnish (NFE) AF: 0.406 AC: 27548 AN: 67920

Other (OTH) AF: 0.318 AC: 670 AN: 2108

Alfa AF: 0.219 Hom.: 586

Bravo AF: 0.293

Asia WGS AF: 0.263 AC: 917 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	1.5
DANN	Benign	0.29
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs2144880; hg19: chr20-59285178;