20-20968220-T-C

Variant names:

• chr20-20968220-T-C
• rs6137194

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.286 in 152,082 control chromosomes in the GnomAD database, including 7,046 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 0.29 (7046 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.879
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 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: 0.286 AC: 43521 AN: 151964 Hom.: 7049 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.286 AC: 43530 AN: 152082 Hom.: 7046 Cov.: 32 AF XY: 0.291 AC XY: 21599 AN XY: 74342

African (AFR) AF: 0.146 AC: 6050 AN: 41506

American (AMR) AF: 0.331 AC: 5057 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1065 AN: 3466

East Asian (EAS) AF: 0.534 AC: 2753 AN: 5156

South Asian (SAS) AF: 0.437 AC: 2104 AN: 4810

European-Finnish (FIN) AF: 0.310 AC: 3287 AN: 10590

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22166 AN: 67970

Other (OTH) AF: 0.306 AC: 647 AN: 2112

Alfa AF: 0.317 Hom.: 33001

Bravo AF: 0.282

Asia WGS AF: 0.438 AC: 1523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	13
DANN	Benign	0.67
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs6137194; hg19: chr20-20948861;