rs3095330

Variant names:

• chr6-30725856-A-G
• rs3095330

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 0.267 in 151,916 control chromosomes in the GnomAD database, including 6,587 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 0.27 (6587 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.28
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 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: 0.267 AC: 40572 AN: 151798 Hom.: 6564 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.267 AC: 40629 AN: 151916 Hom.: 6587 Cov.: 31 AF XY: 0.258 AC XY: 19159 AN XY: 74282

African (AFR) AF: 0.457 AC: 18892 AN: 41354

American (AMR) AF: 0.221 AC: 3368 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3466

East Asian (EAS) AF: 0.199 AC: 1026 AN: 5162

South Asian (SAS) AF: 0.170 AC: 820 AN: 4814

European-Finnish (FIN) AF: 0.104 AC: 1098 AN: 10574

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13956 AN: 67970

Other (OTH) AF: 0.276 AC: 582 AN: 2110

Alfa AF: 0.247 Hom.: 4898

Bravo AF: 0.287

Asia WGS AF: 0.247 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.47
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs3095330; hg19: chr6-30693633;