rs2392467

Variant names:

• chr7-36785685-G-A
• rs2392467

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 0.267 in 152,168 control chromosomes in the GnomAD database, including 5,738 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 0.27 (5738 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40547 AN: 152050 Hom.: 5736 Cov.: 33

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.267 AC: 40582 AN: 152168 Hom.: 5738 Cov.: 33 AF XY: 0.263 AC XY: 19570 AN XY: 74402

African (AFR) AF: 0.344 AC: 14276 AN: 41492

American (AMR) AF: 0.260 AC: 3970 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 958 AN: 3466

East Asian (EAS) AF: 0.176 AC: 914 AN: 5188

South Asian (SAS) AF: 0.272 AC: 1313 AN: 4826

European-Finnish (FIN) AF: 0.127 AC: 1350 AN: 10600

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16937 AN: 67990

Other (OTH) AF: 0.279 AC: 589 AN: 2112

Alfa AF: 0.258 Hom.: 9622

Bravo AF: 0.277

Asia WGS AF: 0.242 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0030
DANN	Benign	0.51
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs2392467; hg19: chr7-36825290;