chr20-47205635-T-C

Position:

• chr20-47205635-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 0.0864 in 152,250 control chromosomes in the GnomAD database, including 727 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 0.086 (727 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0864 AC: 13140 AN: 152132 Hom.: 724 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0506

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.0505

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0512

Gnomad OTH AF: 0.0930

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

GnomAD4 genome AF: 0.0864 AC: 13160 AN: 152250 Hom.: 727 Cov.: 32 AF XY: 0.0887 AC XY: 6602 AN XY: 74460

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0740

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.0505

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.0505

Gnomad4 NFE AF: 0.0513

Gnomad4 OTH AF: 0.0944

Alfa AF: 0.0625 Hom.: 777

Bravo AF: 0.0894

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.89
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7262634; hg19: chr20-45834279;