chr20-48574797-T-C

Position:

• chr20-48574797-T-C

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 0.734 in 151,664 control chromosomes in the GnomAD database, including 41,058 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 0.73 (41058 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111133 AN: 151546 Hom.: 41001 Cov.: 28

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.734 AC: 111251 AN: 151664 Hom.: 41058 Cov.: 28 AF XY: 0.733 AC XY: 54278 AN XY: 74082

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.761

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.698

Alfa AF: 0.686 Hom.: 14080

Bravo AF: 0.738

Asia WGS AF: 0.658 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.44
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6012481; hg19: chr20-47191335;