20-6983435-T-G

Variant names:

• chr20-6983435-T-G
• rs6085806

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 0.548 in 151,946 control chromosomes in the GnomAD database, including 25,632 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 0.55 (25632 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 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: 0.548 AC: 83185 AN: 151828 Hom.: 25633 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.548 AC: 83214 AN: 151946 Hom.: 25632 Cov.: 32 AF XY: 0.556 AC XY: 41259 AN XY: 74252

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.547

Alfa AF: 0.625 Hom.: 27813

Bravo AF: 0.527

Asia WGS AF: 0.661 AC: 2296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6085806; hg19: chr20-6964082;