rs7386474

Variant names:

• chr8-141349451-A-G
• rs7386474

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 0.412 in 151,448 control chromosomes in the GnomAD database, including 13,631 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 (13631 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.982

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.519 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: 0.412 AC: 62378 AN: 151330 Hom.: 13612 Cov.: 30

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.412 AC: 62449 AN: 151448 Hom.: 13631 Cov.: 30 AF XY: 0.412 AC XY: 30474 AN XY: 73958

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.401

Alfa AF: 0.450 Hom.: 10217

Bravo AF: 0.403

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.7
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7386474; hg19: chr8-142359550;