20-6710422-C-T

Position:

• chr20-6710422-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;