20-17057231-C-T

Variant names:

• chr20-17057231-C-T
• rs6075164

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.457 in 152,060 control chromosomes in the GnomAD database, including 16,651 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 0.46 (16651 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 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: 0.457 AC: 69366 AN: 151942 Hom.: 16626 Cov.: 33

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.457 AC: 69439 AN: 152060 Hom.: 16651 Cov.: 33 AF XY: 0.464 AC XY: 34518 AN XY: 74326

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.439

Alfa AF: 0.418 Hom.: 6351

Bravo AF: 0.465

Asia WGS AF: 0.671 AC: 2333 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6075164; hg19: chr20-17037876;