chr7-50588637-G-A

Variant names:

• chr7-50588637-G-A
• rs12669770

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 0.358 in 151,974 control chromosomes in the GnomAD database, including 10,257 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 0.36 (10257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 11 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 (EAS) allele frequency at 95% confidence interval = 0.566 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: 0.358 AC: 54300 AN: 151856 Hom.: 10237 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.358 AC: 54347 AN: 151974 Hom.: 10257 Cov.: 32 AF XY: 0.370 AC XY: 27469 AN XY: 74268

African (AFR) AF: 0.307 AC: 12711 AN: 41436

American (AMR) AF: 0.312 AC: 4768 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3470

East Asian (EAS) AF: 0.584 AC: 3002 AN: 5144

South Asian (SAS) AF: 0.470 AC: 2263 AN: 4820

European-Finnish (FIN) AF: 0.538 AC: 5678 AN: 10548

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23898 AN: 67950

Other (OTH) AF: 0.317 AC: 669 AN: 2112

Alfa AF: 0.343 Hom.: 11621

Bravo AF: 0.340

Asia WGS AF: 0.460 AC: 1601 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	0.57
DANN	Benign	0.74
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12669770; hg19: chr7-50656334;