rs6123568

Variant names:

• chr20-56251582-G-C
• rs6123568

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 0.0398 in 152,266 control chromosomes in the GnomAD database, including 234 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 0.040 (234 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 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: 0.0397 AC: 6036 AN: 152148 Hom.: 229 Cov.: 32

Gnomad AFR AF: 0.0461

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0290

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.0765

Gnomad FIN AF: 0.0356

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0227

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0398 AC: 6058 AN: 152266 Hom.: 234 Cov.: 32 AF XY: 0.0413 AC XY: 3074 AN XY: 74456

African (AFR) AF: 0.0461 AC: 1916 AN: 41552

American (AMR) AF: 0.0290 AC: 444 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3472

East Asian (EAS) AF: 0.233 AC: 1207 AN: 5170

South Asian (SAS) AF: 0.0774 AC: 373 AN: 4822

European-Finnish (FIN) AF: 0.0356 AC: 378 AN: 10610

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0227 AC: 1543 AN: 68022

Other (OTH) AF: 0.0435 AC: 92 AN: 2114

Alfa AF: 0.0311 Hom.: 14

Bravo AF: 0.0402

Asia WGS AF: 0.155 AC: 537 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	4.1
DANN	Benign	0.51
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs6123568; hg19: chr20-54826638;