7-99785313-A-G

Variant names:

• chr7-99785313-A-G
• rs1851426

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 0.779 in 152,212 control chromosomes in the GnomAD database, including 52,519 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 0.78 (52519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 17 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 (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.780 AC: 118585 AN: 152094 Hom.: 52518 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.965

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.779 AC: 118606 AN: 152212 Hom.: 52519 Cov.: 32 AF XY: 0.786 AC XY: 58540 AN XY: 74436

African (AFR) AF: 0.319 AC: 13218 AN: 41478

American (AMR) AF: 0.882 AC: 13496 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.954 AC: 3308 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5168 AN: 5178

South Asian (SAS) AF: 0.970 AC: 4679 AN: 4824

European-Finnish (FIN) AF: 0.964 AC: 10229 AN: 10616

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.965 AC: 65658 AN: 68034

Other (OTH) AF: 0.828 AC: 1751 AN: 2114

Alfa AF: 0.878 Hom.: 121219

Bravo AF: 0.751

Asia WGS AF: 0.936 AC: 3253 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	0.14
DANN	Benign	0.45
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1851426; hg19: chr7-99382936;