rs4814656

Positions:

• chr20-17788895-G-A

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 0.387 in 151,836 control chromosomes in the GnomAD database, including 11,952 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 0.39 (11952 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 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: 0.387 AC: 58692 AN: 151718 Hom.: 11947 Cov.: 31

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.387 AC: 58733 AN: 151836 Hom.: 11952 Cov.: 31 AF XY: 0.391 AC XY: 29039 AN XY: 74196

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.373

Alfa AF: 0.396 Hom.: 2072

Bravo AF: 0.370

Asia WGS AF: 0.366 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4814656; hg19: chr20-17769540;