rs6798973

Variant names:

• chr3-184466447-G-A
• rs6798973

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 0.133 in 152,230 control chromosomes in the GnomAD database, including 1,525 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 0.13 (1525 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.857
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 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: 0.133 AC: 20299 AN: 152112 Hom.: 1521 Cov.: 33

Gnomad AFR AF: 0.0979

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0288

Gnomad SAS AF: 0.0401

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.133 AC: 20315 AN: 152230 Hom.: 1525 Cov.: 33 AF XY: 0.129 AC XY: 9581 AN XY: 74414

African (AFR) AF: 0.0979 AC: 4069 AN: 41554

American (AMR) AF: 0.131 AC: 2007 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 904 AN: 3468

East Asian (EAS) AF: 0.0287 AC: 148 AN: 5162

South Asian (SAS) AF: 0.0412 AC: 199 AN: 4834

European-Finnish (FIN) AF: 0.123 AC: 1308 AN: 10610

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11056 AN: 67972

Other (OTH) AF: 0.154 AC: 325 AN: 2114

Alfa AF: 0.156 Hom.: 7282

Bravo AF: 0.134

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.45
DANN	Benign	0.62
PhyloP100		-0.86
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6798973; hg19: chr3-184184235;