20-201372-T-C

Variant names:

• chr20-201372-T-C
• rs6078500

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 0.503 in 152,010 control chromosomes in the GnomAD database, including 19,230 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 0.50 (19230 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.597 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: 0.503 AC: 76381 AN: 151894 Hom.: 19205 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.503 AC: 76444 AN: 152010 Hom.: 19230 Cov.: 32 AF XY: 0.505 AC XY: 37512 AN XY: 74284

African (AFR) AF: 0.482 AC: 19966 AN: 41458

American (AMR) AF: 0.488 AC: 7447 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1744 AN: 3470

East Asian (EAS) AF: 0.533 AC: 2745 AN: 5154

South Asian (SAS) AF: 0.615 AC: 2956 AN: 4806

European-Finnish (FIN) AF: 0.494 AC: 5219 AN: 10556

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34811 AN: 67982

Other (OTH) AF: 0.457 AC: 965 AN: 2112

Alfa AF: 0.499 Hom.: 45181

Bravo AF: 0.497

Asia WGS AF: 0.516 AC: 1797 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	0.90
DANN	Benign	0.37
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6078500; hg19: chr20-182013;