rs4866550

Variant names:

• chr5-3308198-T-C
• rs4866550

Your query was ambiguous. Multiple possible variants found:

• chr5-3308198-T-C
• chr5-3308198-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 0.638 in 151,958 control chromosomes in the GnomAD database, including 31,350 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 0.64 (31350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96837 AN: 151842 Hom.: 31335 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.638 AC: 96895 AN: 151958 Hom.: 31350 Cov.: 32 AF XY: 0.642 AC XY: 47698 AN XY: 74264

African (AFR) AF: 0.513 AC: 21284 AN: 41454

American (AMR) AF: 0.647 AC: 9897 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2308 AN: 3466

East Asian (EAS) AF: 0.784 AC: 4022 AN: 5132

South Asian (SAS) AF: 0.686 AC: 3306 AN: 4816

European-Finnish (FIN) AF: 0.724 AC: 7633 AN: 10550

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.683 AC: 46374 AN: 67938

Other (OTH) AF: 0.623 AC: 1318 AN: 2114

Alfa AF: 0.664 Hom.: 139749

Bravo AF: 0.625

Asia WGS AF: 0.694 AC: 2414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.056
DANN	Benign	0.53
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4866550; hg19: chr5-3308312;