rs2077713

Variant names:

• chr20-238142-T-C
• rs2077713

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 0.274 in 152,126 control chromosomes in the GnomAD database, including 9,441 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 0.27 (9441 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 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: 0.274 AC: 41693 AN: 152008 Hom.: 9428 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.274 AC: 41742 AN: 152126 Hom.: 9441 Cov.: 32 AF XY: 0.271 AC XY: 20129 AN XY: 74384

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.220

Alfa AF: 0.252 Hom.: 1220

Bravo AF: 0.290

Asia WGS AF: 0.250 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.3
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2077713; hg19: chr20-218783;