7-55787487-G-A

Variant names:

• chr7-55787487-G-A
• rs11982736

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 0.338 in 151,398 control chromosomes in the GnomAD database, including 12,531 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 0.34 (12531 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 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: 0.338 AC: 51080 AN: 151294 Hom.: 12494 Cov.: 30

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.338 AC: 51169 AN: 151398 Hom.: 12531 Cov.: 30 AF XY: 0.340 AC XY: 25135 AN XY: 73948

African (AFR) AF: 0.685 AC: 28274 AN: 41266

American (AMR) AF: 0.282 AC: 4281 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3468

East Asian (EAS) AF: 0.456 AC: 2333 AN: 5120

South Asian (SAS) AF: 0.368 AC: 1760 AN: 4778

European-Finnish (FIN) AF: 0.232 AC: 2409 AN: 10402

Middle Eastern (MID) AF: 0.241 AC: 70 AN: 290

European-Non Finnish (NFE) AF: 0.159 AC: 10790 AN: 67856

Other (OTH) AF: 0.292 AC: 615 AN: 2108

Alfa AF: 0.227 Hom.: 15782

Bravo AF: 0.356

Asia WGS AF: 0.409 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.7
DANN	Benign	0.63
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs11982736; hg19: chr7-55855180;