rs4729607

Variant names:

• chr7-100729121-T-A
• rs4729607

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 0.215 in 152,154 control chromosomes in the GnomAD database, including 3,584 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 0.22 (3584 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 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: 0.215 AC: 32729 AN: 152036 Hom.: 3575 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.215 AC: 32769 AN: 152154 Hom.: 3584 Cov.: 32 AF XY: 0.211 AC XY: 15730 AN XY: 74406

African (AFR) AF: 0.186 AC: 7722 AN: 41502

American (AMR) AF: 0.184 AC: 2804 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3470

East Asian (EAS) AF: 0.144 AC: 746 AN: 5184

South Asian (SAS) AF: 0.137 AC: 660 AN: 4828

European-Finnish (FIN) AF: 0.266 AC: 2816 AN: 10592

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16644 AN: 67988

Other (OTH) AF: 0.189 AC: 399 AN: 2112

Alfa AF: 0.239 Hom.: 557

Bravo AF: 0.211

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.3
DANN	Benign	0.59
PhyloP100		0.054

Splicing

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

Other links and lift over

dbSNP: rs4729607; hg19: chr7-100326744;