rs868082

Variant names:

• chr4-183359791-G-A
• rs868082

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 0.0838 in 152,184 control chromosomes in the GnomAD database, including 618 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 0.084 (618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 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: 0.0837 AC: 12735 AN: 152066 Hom.: 615 Cov.: 32

Gnomad AFR AF: 0.0560

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0621

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.00944

Gnomad SAS AF: 0.0558

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.0838 AC: 12750 AN: 152184 Hom.: 618 Cov.: 32 AF XY: 0.0823 AC XY: 6121 AN XY: 74380

African (AFR) AF: 0.0562 AC: 2333 AN: 41534

American (AMR) AF: 0.0625 AC: 956 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3468

East Asian (EAS) AF: 0.00946 AC: 49 AN: 5178

South Asian (SAS) AF: 0.0556 AC: 268 AN: 4818

European-Finnish (FIN) AF: 0.112 AC: 1187 AN: 10566

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7523 AN: 67992

Other (OTH) AF: 0.0842 AC: 178 AN: 2114

Alfa AF: 0.0989 Hom.: 1464

Bravo AF: 0.0781

Asia WGS AF: 0.0530 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.34
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs868082; hg19: chr4-184280944;