rs3848711

Variant names:

• chr20-45817461-G-A
• rs3848711

Your query was ambiguous. Multiple possible variants found:

• chr20-45817461-G-A
• chr20-45817461-G-C

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 0.508 in 152,098 control chromosomes in the GnomAD database, including 20,229 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 0.51 (20229 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.566 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: 0.508 AC: 77247 AN: 151980 Hom.: 20210 Cov.: 33

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.508 AC: 77297 AN: 152098 Hom.: 20229 Cov.: 33 AF XY: 0.507 AC XY: 37723 AN XY: 74364

African (AFR) AF: 0.386 AC: 16015 AN: 41498

American (AMR) AF: 0.534 AC: 8172 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1422 AN: 3468

East Asian (EAS) AF: 0.526 AC: 2714 AN: 5158

South Asian (SAS) AF: 0.434 AC: 2092 AN: 4824

European-Finnish (FIN) AF: 0.603 AC: 6384 AN: 10594

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38764 AN: 67946

Other (OTH) AF: 0.507 AC: 1069 AN: 2110

Alfa AF: 0.520 Hom.: 2660

Bravo AF: 0.501

Asia WGS AF: 0.463 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.99
DANN	Benign	0.50
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs3848711; hg19: chr20-44446100;