chr7-30906312-A-C

Position:

• chr7-30906312-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 0.298 in 152,120 control chromosomes in the GnomAD database, including 9,569 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 0.30 (9569 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.887

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 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: 0.298 AC: 45237 AN: 152002 Hom.: 9523 Cov.: 33

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.298 AC: 45344 AN: 152120 Hom.: 9569 Cov.: 33 AF XY: 0.298 AC XY: 22151 AN XY: 74374

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.258

Alfa AF: 0.185 Hom.: 1529

Bravo AF: 0.314

Asia WGS AF: 0.315 AC: 1097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	14
DANN	Benign	0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7788618; hg19: chr7-30945927;