7-128928906-A-C

Position:

• chr7-128928906-A-C

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 0.28 in 152,068 control chromosomes in the GnomAD database, including 6,444 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 (6444 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42603 AN: 151950 Hom.: 6443 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.280 AC: 42619 AN: 152068 Hom.: 6444 Cov.: 32 AF XY: 0.283 AC XY: 21004 AN XY: 74322

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.255

Alfa AF: 0.317 Hom.: 16188

Bravo AF: 0.267

Asia WGS AF: 0.307 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs729302; hg19: chr7-128568960;