rs7442317

Variant names:

• chr4-29901430-G-A
• rs7442317

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 0.32 in 151,978 control chromosomes in the GnomAD database, including 8,419 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 0.32 (8419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 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: 0.319 AC: 48505 AN: 151860 Hom.: 8397 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.320 AC: 48570 AN: 151978 Hom.: 8419 Cov.: 32 AF XY: 0.314 AC XY: 23302 AN XY: 74288

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.313

Alfa AF: 0.278 Hom.: 11565

Bravo AF: 0.326

Asia WGS AF: 0.349 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7442317; hg19: chr4-29903052;