rs6798973

Positions:

• chr3-184466447-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0979

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.0287

Gnomad4 SAS AF: 0.0412

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.154

Alfa AF: 0.163 Hom.: 3155

Bravo AF: 0.134

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.45
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6798973; hg19: chr3-184184235;