7-127284699-G-A

Variant names:

• chr7-127284699-G-A
• rs1419391

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 0.594 in 151,942 control chromosomes in the GnomAD database, including 29,875 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 0.59 (29875 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 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: 0.594 AC: 90119 AN: 151824 Hom.: 29828 Cov.: 31

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.594 AC: 90210 AN: 151942 Hom.: 29875 Cov.: 31 AF XY: 0.583 AC XY: 43260 AN XY: 74250

African (AFR) AF: 0.895 AC: 37153 AN: 41496

American (AMR) AF: 0.532 AC: 8116 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2378 AN: 3466

East Asian (EAS) AF: 0.256 AC: 1325 AN: 5170

South Asian (SAS) AF: 0.409 AC: 1968 AN: 4806

European-Finnish (FIN) AF: 0.393 AC: 4118 AN: 10482

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33141 AN: 67944

Other (OTH) AF: 0.606 AC: 1281 AN: 2114

Alfa AF: 0.523 Hom.: 66680

Bravo AF: 0.619

Asia WGS AF: 0.391 AC: 1362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.58
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1419391; hg19: chr7-126924753;