chr6-30077050-C-T

Variant names:

• chr6-30077050-C-T
• rs3807035

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 151,930 control chromosomes in the GnomAD database, including 6,011 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 (6011 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 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: 0.241 AC: 36544 AN: 151812 Hom.: 5991 Cov.: 31

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.0510

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.241 AC: 36603 AN: 151930 Hom.: 6011 Cov.: 31 AF XY: 0.236 AC XY: 17505 AN XY: 74280

African (AFR) AF: 0.454 AC: 18766 AN: 41368

American (AMR) AF: 0.266 AC: 4064 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1202 AN: 3468

East Asian (EAS) AF: 0.191 AC: 986 AN: 5156

South Asian (SAS) AF: 0.194 AC: 935 AN: 4814

European-Finnish (FIN) AF: 0.0510 AC: 539 AN: 10570

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9428 AN: 67972

Other (OTH) AF: 0.274 AC: 575 AN: 2102

Alfa AF: 0.177 Hom.: 13030

Bravo AF: 0.271

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.7
DANN	Benign	0.72
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs3807035; hg19: chr6-30044827;