rs4810796

chr20-48459954-G-Achr20-48459954-G-C

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 0.319 in 151,908 control chromosomes in the GnomAD database, including 8,172 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 0.32 (8172 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 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: 0.319 AC: 48346 AN: 151790 Hom.: 8158 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.319 AC: 48389 AN: 151908 Hom.: 8172 Cov.: 32 AF XY: 0.328 AC XY: 24345 AN XY: 74236

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.302

Alfa AF: 0.295 Hom.: 5506

Bravo AF: 0.327

Asia WGS AF: 0.405 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.71
Dann	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4810796; hg19: chr20-47088200;