chr20-12241517-G-C

Variant names:

• chr20-12241517-G-C
• rs6134479

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 0.173 in 152,208 control chromosomes in the GnomAD database, including 2,834 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 0.17 (2834 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 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: 0.174 AC: 26400 AN: 152090 Hom.: 2833 Cov.: 33

Gnomad AFR AF: 0.0439

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.173 AC: 26390 AN: 152208 Hom.: 2834 Cov.: 33 AF XY: 0.170 AC XY: 12677 AN XY: 74400

African (AFR) AF: 0.0437 AC: 1817 AN: 41560

American (AMR) AF: 0.191 AC: 2916 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3472

East Asian (EAS) AF: 0.200 AC: 1034 AN: 5168

South Asian (SAS) AF: 0.120 AC: 578 AN: 4822

European-Finnish (FIN) AF: 0.176 AC: 1860 AN: 10594

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16479 AN: 67994

Other (OTH) AF: 0.205 AC: 433 AN: 2108

Alfa AF: 0.0872 Hom.: 113

Bravo AF: 0.173

Asia WGS AF: 0.146 AC: 509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.48
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs6134479; hg19: chr20-12222165;