7-46580547-A-G

Variant names:

• chr7-46580547-A-G
• rs7784776

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 0.424 in 151,914 control chromosomes in the GnomAD database, including 14,126 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 0.42 (14126 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 29 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 = 0.739 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: 0.424 AC: 64376 AN: 151796 Hom.: 14118 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.424 AC: 64418 AN: 151914 Hom.: 14126 Cov.: 32 AF XY: 0.425 AC XY: 31554 AN XY: 74262

African (AFR) AF: 0.407 AC: 16833 AN: 41404

American (AMR) AF: 0.475 AC: 7251 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1505 AN: 3468

East Asian (EAS) AF: 0.759 AC: 3904 AN: 5142

South Asian (SAS) AF: 0.444 AC: 2138 AN: 4820

European-Finnish (FIN) AF: 0.352 AC: 3708 AN: 10542

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.405 AC: 27504 AN: 67974

Other (OTH) AF: 0.459 AC: 970 AN: 2114

Alfa AF: 0.423 Hom.: 60631

Bravo AF: 0.436

Asia WGS AF: 0.547 AC: 1899 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	0.91
DANN	Benign	0.29
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs7784776; hg19: chr7-46620145;