chr20-17057231-C-T

Variant names:

• chr20-17057231-C-T
• rs6075164

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 0.457 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
• Publications: 3 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 (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

African (AFR) AF: 0.467 AC: 19348 AN: 41460

American (AMR) AF: 0.557 AC: 8517 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1448 AN: 3470

East Asian (EAS) AF: 0.842 AC: 4358 AN: 5178

South Asian (SAS) AF: 0.521 AC: 2516 AN: 4826

European-Finnish (FIN) AF: 0.467 AC: 4930 AN: 10552

Middle Eastern (MID) AF: 0.366 AC: 106 AN: 290

European-Non Finnish (NFE) AF: 0.398 AC: 27049 AN: 67970

Other (OTH) AF: 0.439 AC: 927 AN: 2114

Alfa AF: 0.416 Hom.: 6956

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6075164; hg19: chr20-17037876;