rs7442317

Variant names:

• chr4-29901430-G-A
• rs7442317

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 0.32 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.470 AC: 19484 AN: 41432

American (AMR) AF: 0.216 AC: 3302 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 974 AN: 3470

East Asian (EAS) AF: 0.374 AC: 1927 AN: 5158

South Asian (SAS) AF: 0.268 AC: 1289 AN: 4816

European-Finnish (FIN) AF: 0.236 AC: 2492 AN: 10560

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18173 AN: 67950

Other (OTH) AF: 0.313 AC: 660 AN: 2112

Alfa AF: 0.287 Hom.: 19728

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs7442317; hg19: chr4-29903052;