rs4456770

Positions:

• chr20-6671503-G-A
• chr20-6671503-G-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 0.398 in 151,874 control chromosomes in the GnomAD database, including 13,104 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 0.40 (13104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.535

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60350 AN: 151756 Hom.: 13101 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.398 AC: 60372 AN: 151874 Hom.: 13104 Cov.: 32 AF XY: 0.389 AC XY: 28833 AN XY: 74206

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.391

Alfa AF: 0.471 Hom.: 16272

Bravo AF: 0.390

Asia WGS AF: 0.216 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.0
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4456770; hg19: chr20-6652150;