rs4810083

Variant names:

• chr20-57545215-T-C
• rs4810083

Your query was ambiguous. Multiple possible variants found:

• chr20-57545215-T-C
• chr20-57545215-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.548 in 151,934 control chromosomes in the GnomAD database, including 23,141 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 0.55 (23141 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 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: 0.548 AC: 83221 AN: 151816 Hom.: 23145 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.548 AC: 83236 AN: 151934 Hom.: 23141 Cov.: 32 AF XY: 0.545 AC XY: 40466 AN XY: 74268

African (AFR) AF: 0.594 AC: 24586 AN: 41416

American (AMR) AF: 0.451 AC: 6879 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1963 AN: 3466

East Asian (EAS) AF: 0.473 AC: 2445 AN: 5170

South Asian (SAS) AF: 0.452 AC: 2167 AN: 4796

European-Finnish (FIN) AF: 0.569 AC: 6008 AN: 10558

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37288 AN: 67964

Other (OTH) AF: 0.562 AC: 1186 AN: 2110

Alfa AF: 0.542 Hom.: 30493

Bravo AF: 0.544

Asia WGS AF: 0.447 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.041
DANN	Benign	0.40
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4810083; hg19: chr20-56120271;