20-6601515-C-T

Variant names:

• chr20-6601515-C-T
• rs6140038

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0217 in 152,308 control chromosomes in the GnomAD database, including 51 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 0.022 (51 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0217 (3302/152308) while in subpopulation EAS AF = 0.0539 (280/5192). AF 95% confidence interval is 0.0487. There are 51 homozygotes in GnomAd4. There are 1526 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 51 gene

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: 0.0217 AC: 3302 AN: 152190 Hom.: 51 Cov.: 33

Gnomad AFR AF: 0.00606

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0268

Gnomad ASJ AF: 0.0354

Gnomad EAS AF: 0.0540

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0105

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0288

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0217 AC: 3302 AN: 152308 Hom.: 51 Cov.: 33 AF XY: 0.0205 AC XY: 1526 AN XY: 74470

African (AFR) AF: 0.00604 AC: 251 AN: 41564

American (AMR) AF: 0.0269 AC: 411 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0354 AC: 123 AN: 3470

East Asian (EAS) AF: 0.0539 AC: 280 AN: 5192

South Asian (SAS) AF: 0.0166 AC: 80 AN: 4820

European-Finnish (FIN) AF: 0.0105 AC: 112 AN: 10618

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0288 AC: 1961 AN: 68024

Other (OTH) AF: 0.0350 AC: 74 AN: 2116

Alfa AF: 0.0184 Hom.: 11

Bravo AF: 0.0221

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.6
DANN	Benign	0.63
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs6140038; hg19: chr20-6582162;