20-48591688-T-C

Variant names:

• chr20-48591688-T-C
• rs6090875

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 0.192 in 152,064 control chromosomes in the GnomAD database, including 3,154 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 0.19 (3154 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.231 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: 0.192 AC: 29140 AN: 151946 Hom.: 3155 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.0970

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.192 AC: 29158 AN: 152064 Hom.: 3154 Cov.: 32 AF XY: 0.190 AC XY: 14152 AN XY: 74342

Gnomad4 AFR AF: 0.0980

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.0968

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.218

Alfa AF: 0.213 Hom.: 1086

Bravo AF: 0.188

Asia WGS AF: 0.144 AC: 499 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	11
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6090875; hg19: chr20-47208226;