rs3807033

Variant names:

• chr6-30076178-G-A
• rs3807033

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.189 in 151,982 control chromosomes in the GnomAD database, including 4,244 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 0.19 (4244 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.608
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 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: 0.189 AC: 28644 AN: 151866 Hom.: 4236 Cov.: 33

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0266

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.0869

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.189 AC: 28682 AN: 151982 Hom.: 4244 Cov.: 33 AF XY: 0.184 AC XY: 13654 AN XY: 74320

African (AFR) AF: 0.404 AC: 16746 AN: 41430

American (AMR) AF: 0.198 AC: 3025 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 597 AN: 3436

East Asian (EAS) AF: 0.152 AC: 783 AN: 5162

South Asian (SAS) AF: 0.170 AC: 823 AN: 4830

European-Finnish (FIN) AF: 0.0266 AC: 282 AN: 10618

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.0869 AC: 5903 AN: 67930

Other (OTH) AF: 0.210 AC: 444 AN: 2112

Alfa AF: 0.122 Hom.: 3801

Bravo AF: 0.216

Asia WGS AF: 0.162 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	19
DANN	Benign	0.86
PhyloP100		0.61
PromoterAI		-0.15	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3807033; hg19: chr6-30043955;