chr7-129574333-G-A

Variant names:

• chr7-129574333-G-A
• rs754386

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.180 AC: 7480 AN: 41492

American (AMR) AF: 0.112 AC: 1718 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 410 AN: 3470

East Asian (EAS) AF: 0.131 AC: 679 AN: 5168

South Asian (SAS) AF: 0.160 AC: 772 AN: 4820

European-Finnish (FIN) AF: 0.151 AC: 1592 AN: 10578

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.134 AC: 9109 AN: 67990

Other (OTH) AF: 0.158 AC: 334 AN: 2114

Alfa AF: 0.138 Hom.: 2894

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
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs754386; hg19: chr7-129214174;