20-6710422-C-T

Variant names:

• chr20-6710422-C-T
• rs6085660

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 0.415 in 152,024 control chromosomes in the GnomAD database, including 13,618 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 0.41 (13618 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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: 0.415 AC: 62980 AN: 151908 Hom.: 13605 Cov.: 33

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.415 AC: 63034 AN: 152024 Hom.: 13618 Cov.: 33 AF XY: 0.421 AC XY: 31256 AN XY: 74292

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.412

Alfa AF: 0.410 Hom.: 7134

Bravo AF: 0.418

Asia WGS AF: 0.591 AC: 2056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.12
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6085660; hg19: chr20-6691069;