7-46236130-A-G

Variant names:

• chr7-46236130-A-G
• rs1486139

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 0.461 in 151,958 control chromosomes in the GnomAD database, including 18,077 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 0.46 (18077 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.66 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: 0.461 AC: 69993 AN: 151840 Hom.: 18078 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.461 AC: 70000 AN: 151958 Hom.: 18077 Cov.: 32 AF XY: 0.468 AC XY: 34758 AN XY: 74282

African (AFR) AF: 0.211 AC: 8758 AN: 41486

American (AMR) AF: 0.528 AC: 8069 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2012 AN: 3468

East Asian (EAS) AF: 0.679 AC: 3496 AN: 5150

South Asian (SAS) AF: 0.518 AC: 2501 AN: 4824

European-Finnish (FIN) AF: 0.575 AC: 6062 AN: 10534

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.548 AC: 37218 AN: 67914

Other (OTH) AF: 0.523 AC: 1105 AN: 2112

Alfa AF: 0.512 Hom.: 38673

Bravo AF: 0.446

Asia WGS AF: 0.566 AC: 1970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.70
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs1486139; hg19: chr7-46275728;