7-55302519-G-A

Variant names:

• chr7-55302519-G-A
• rs4948007

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 0.21 in 152,056 control chromosomes in the GnomAD database, including 4,275 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 0.21 (4275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.34 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: 0.210 AC: 31934 AN: 151938 Hom.: 4255 Cov.: 32

Gnomad AFR AF: 0.0557

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.210 AC: 31967 AN: 152056 Hom.: 4275 Cov.: 32 AF XY: 0.214 AC XY: 15896 AN XY: 74334

African (AFR) AF: 0.0555 AC: 2304 AN: 41478

American (AMR) AF: 0.347 AC: 5302 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1358 AN: 3472

East Asian (EAS) AF: 0.335 AC: 1729 AN: 5158

South Asian (SAS) AF: 0.224 AC: 1076 AN: 4810

European-Finnish (FIN) AF: 0.231 AC: 2443 AN: 10574

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.250 AC: 17019 AN: 67992

Other (OTH) AF: 0.246 AC: 518 AN: 2104

Alfa AF: 0.252 Hom.: 6461

Bravo AF: 0.216

Asia WGS AF: 0.273 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.85
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4948007; hg19: chr7-55370212;