7-28272444-G-C

Variant names:

• chr7-28272444-G-C
• rs4722778

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.272 in 152,116 control chromosomes in the GnomAD database, including 6,626 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 0.27 (6626 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 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: 0.272 AC: 41389 AN: 151998 Hom.: 6620 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.272 AC: 41406 AN: 152116 Hom.: 6626 Cov.: 33 AF XY: 0.281 AC XY: 20889 AN XY: 74374

African (AFR) AF: 0.167 AC: 6919 AN: 41502

American (AMR) AF: 0.336 AC: 5138 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 748 AN: 3468

East Asian (EAS) AF: 0.710 AC: 3673 AN: 5176

South Asian (SAS) AF: 0.431 AC: 2083 AN: 4832

European-Finnish (FIN) AF: 0.343 AC: 3622 AN: 10566

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.267 AC: 18122 AN: 67974

Other (OTH) AF: 0.275 AC: 581 AN: 2112

Alfa AF: 0.169 Hom.: 378

Bravo AF: 0.269

Asia WGS AF: 0.522 AC: 1811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	13
DANN	Benign	0.70
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs4722778; hg19: chr7-28312063;