rs6089055

Variant names:

• chr20-31736242-C-T
• rs6089055

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 0.175 in 151,928 control chromosomes in the GnomAD database, including 2,755 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 0.18 (2755 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 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: 0.175 AC: 26589 AN: 151808 Hom.: 2756 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0597

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.175 AC: 26589 AN: 151928 Hom.: 2755 Cov.: 31 AF XY: 0.177 AC XY: 13113 AN XY: 74258

African (AFR) AF: 0.106 AC: 4375 AN: 41448

American (AMR) AF: 0.161 AC: 2453 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3472

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5170

South Asian (SAS) AF: 0.0605 AC: 291 AN: 4806

European-Finnish (FIN) AF: 0.319 AC: 3365 AN: 10540

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14752 AN: 67922

Other (OTH) AF: 0.181 AC: 381 AN: 2110

Alfa AF: 0.200 Hom.: 421

Bravo AF: 0.163

Asia WGS AF: 0.0350 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.62
DANN	Benign	0.60
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs6089055; hg19: chr20-30324045;