rs1863984

Variant names:

• chr5-4211769-A-G
• rs1863984

Your query was ambiguous. Multiple possible variants found:

• chr5-4211769-A-G
• chr5-4211769-A-T

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 0.934 in 152,290 control chromosomes in the GnomAD database, including 66,536 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 0.93 (66536 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.934 AC: 142136 AN: 152172 Hom.: 66476 Cov.: 32

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.934 AC: 142256 AN: 152290 Hom.: 66536 Cov.: 32 AF XY: 0.937 AC XY: 69751 AN XY: 74454

African (AFR) AF: 0.980 AC: 40739 AN: 41574

American (AMR) AF: 0.944 AC: 14429 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 3116 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5172 AN: 5174

South Asian (SAS) AF: 0.968 AC: 4673 AN: 4828

European-Finnish (FIN) AF: 0.929 AC: 9859 AN: 10612

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.900 AC: 61229 AN: 68018

Other (OTH) AF: 0.917 AC: 1941 AN: 2116

Alfa AF: 0.924 Hom.: 51645

Bravo AF: 0.935

Asia WGS AF: 0.985 AC: 3425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.50
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1863984; hg19: chr5-4211882;