rs4729329

Positions:

• chr7-97106447-A-T

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 0.151 in 152,192 control chromosomes in the GnomAD database, including 1,985 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 (1985 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 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: 0.151 AC: 22888 AN: 152074 Hom.: 1983 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.151 AC: 22914 AN: 152192 Hom.: 1985 Cov.: 32 AF XY: 0.156 AC XY: 11605 AN XY: 74388

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.162

Alfa AF: 0.130 Hom.: 167

Bravo AF: 0.161

Asia WGS AF: 0.300 AC: 1042 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.9
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4729329; hg19: chr7-96735759;