rs7429875

Variant names:

• chr3-27548931-T-C
• rs7429875

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 0.413 in 152,036 control chromosomes in the GnomAD database, including 15,906 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 0.41 (15906 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 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: 0.413 AC: 62678 AN: 151918 Hom.: 15856 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.413 AC: 62793 AN: 152036 Hom.: 15906 Cov.: 32 AF XY: 0.408 AC XY: 30288 AN XY: 74320

African (AFR) AF: 0.722 AC: 29939 AN: 41466

American (AMR) AF: 0.290 AC: 4424 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 966 AN: 3466

East Asian (EAS) AF: 0.157 AC: 810 AN: 5174

South Asian (SAS) AF: 0.265 AC: 1279 AN: 4826

European-Finnish (FIN) AF: 0.352 AC: 3714 AN: 10550

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20553 AN: 67956

Other (OTH) AF: 0.359 AC: 758 AN: 2112

Alfa AF: 0.320 Hom.: 14606

Bravo AF: 0.423

Asia WGS AF: 0.306 AC: 1065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.14
DANN	Benign	0.41
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7429875; hg19: chr3-27590422;