6-30904120-T-A

Variant names:

• chr6-30904120-T-A
• rs1264314

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.21 (103 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.207 AC: 3130 AN: 15122 Hom.: 101 Cov.: 0

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0962

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.0385

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.207 AC: 3143 AN: 15158 Hom.: 103 Cov.: 0 AF XY: 0.213 AC XY: 1539 AN XY: 7216

African (AFR) AF: 0.189 AC: 937 AN: 4952

American (AMR) AF: 0.0953 AC: 184 AN: 1930

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 48 AN: 324

East Asian (EAS) AF: 0.0958 AC: 41 AN: 428

South Asian (SAS) AF: 0.222 AC: 82 AN: 370

European-Finnish (FIN) AF: 0.231 AC: 185 AN: 800

Middle Eastern (MID) AF: 0.0417 AC: 1 AN: 24

European-Non Finnish (NFE) AF: 0.267 AC: 1615 AN: 6052

Other (OTH) AF: 0.180 AC: 35 AN: 194

Alfa AF: 0.147 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.56
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs1264314; hg19: chr6-30871897;