6-30377341-C-T

Variant names:

• chr6-30377341-C-T
• rs3132630

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 0.105 in 152,080 control chromosomes in the GnomAD database, including 1,030 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 0.10 (1030 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538
• Publications: 19 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 (AFR) allele frequency at 95% confidence interval = 0.139 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: 0.105 AC: 15890 AN: 151962 Hom.: 1027 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0628

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.0708

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.0822

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

GnomAD4 genome AF: 0.105 AC: 15908 AN: 152080 Hom.: 1030 Cov.: 32 AF XY: 0.0974 AC XY: 7240 AN XY: 74342

African (AFR) AF: 0.142 AC: 5893 AN: 41446

American (AMR) AF: 0.0627 AC: 958 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0470 AC: 163 AN: 3466

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5182

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4826

European-Finnish (FIN) AF: 0.0708 AC: 749 AN: 10580

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7799 AN: 67980

Other (OTH) AF: 0.0814 AC: 172 AN: 2114

Alfa AF: 0.111 Hom.: 2681

Bravo AF: 0.107

Asia WGS AF: 0.0140 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.89
DANN	Benign	0.45
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs3132630; hg19: chr6-30345118;