chr20-7771719-C-T

Variant names:

• chr20-7771719-C-T
• rs6077251

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 0.125 in 151,858 control chromosomes in the GnomAD database, including 1,536 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 0.12 (1536 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.295 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: 0.125 AC: 18923 AN: 151742 Hom.: 1527 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.0615

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.125 AC: 18955 AN: 151858 Hom.: 1536 Cov.: 32 AF XY: 0.127 AC XY: 9392 AN XY: 74198

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.0615

Gnomad4 NFE AF: 0.0896

Gnomad4 OTH AF: 0.148

Alfa AF: 0.103 Hom.: 1981

Bravo AF: 0.133

Asia WGS AF: 0.261 AC: 905 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6077251; hg19: chr20-7752366;