7-129574333-G-A

Position:

• chr7-129574333-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 0.146 in 152,110 control chromosomes in the GnomAD database, including 1,676 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 0.15 (1676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.81

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 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: 0.147 AC: 22277 AN: 151994 Hom.: 1677 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.146 AC: 22280 AN: 152110 Hom.: 1676 Cov.: 32 AF XY: 0.148 AC XY: 11007 AN XY: 74376

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.158

Alfa AF: 0.138 Hom.: 2113

Bravo AF: 0.145

Asia WGS AF: 0.151 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs754386; hg19: chr7-129214174;