chr7-28921704-G-A

Position:

• chr7-28921704-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.276 in 151,926 control chromosomes in the GnomAD database, including 6,585 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 0.28 (6585 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41793 AN: 151808 Hom.: 6563 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0977

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.276 AC: 41866 AN: 151926 Hom.: 6585 Cov.: 32 AF XY: 0.273 AC XY: 20303 AN XY: 74246

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.0980

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.249

Alfa AF: 0.217 Hom.: 7623

Bravo AF: 0.283

Asia WGS AF: 0.216 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.10
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1006514; hg19: chr7-28961321;