rs3873334

Variant names:

• chr6-30928370-G-A
• rs3873334

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 0.241 in 151,836 control chromosomes in the GnomAD database, including 5,265 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 0.24 (5265 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929
• Publications: 25 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 = 0.57 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: 0.241 AC: 36541 AN: 151718 Hom.: 5251 Cov.: 29

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.241 AC: 36581 AN: 151836 Hom.: 5265 Cov.: 29 AF XY: 0.252 AC XY: 18704 AN XY: 74210

African (AFR) AF: 0.241 AC: 9975 AN: 41372

American (AMR) AF: 0.358 AC: 5460 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3466

East Asian (EAS) AF: 0.588 AC: 3026 AN: 5148

South Asian (SAS) AF: 0.498 AC: 2393 AN: 4810

European-Finnish (FIN) AF: 0.250 AC: 2635 AN: 10530

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11428 AN: 67952

Other (OTH) AF: 0.241 AC: 510 AN: 2112

Alfa AF: 0.198 Hom.: 10903

Bravo AF: 0.245

Asia WGS AF: 0.541 AC: 1879 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	1.7
DANN	Benign	0.76
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs3873334; hg19: chr6-30896147;