rs3807036

Variant names:

• chr6-30077137-G-A
• rs3807036

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 0.052 in 152,108 control chromosomes in the GnomAD database, including 255 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 0.052 (255 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0645 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0519 AC: 7892 AN: 151990 Hom.: 254 Cov.: 31

Gnomad AFR AF: 0.0495

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0677

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0357

Gnomad SAS AF: 0.0239

Gnomad FIN AF: 0.0240

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0515

Gnomad OTH AF: 0.0599

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

GnomAD4 genome AF: 0.0520 AC: 7906 AN: 152108 Hom.: 255 Cov.: 31 AF XY: 0.0518 AC XY: 3849 AN XY: 74360

African (AFR) AF: 0.0496 AC: 2056 AN: 41484

American (AMR) AF: 0.0680 AC: 1038 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 605 AN: 3466

East Asian (EAS) AF: 0.0358 AC: 185 AN: 5170

South Asian (SAS) AF: 0.0239 AC: 115 AN: 4816

European-Finnish (FIN) AF: 0.0240 AC: 254 AN: 10584

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0515 AC: 3500 AN: 68004

Other (OTH) AF: 0.0588 AC: 124 AN: 2108

Alfa AF: 0.0559 Hom.: 709

Bravo AF: 0.0545

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.62
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs3807036; hg19: chr6-30044914;