rs7828042

chr8-142737965-A-G

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 0.337 in 151,886 control chromosomes in the GnomAD database, including 8,948 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 0.34 (8948 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51169 AN: 151766 Hom.: 8937 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.337 AC: 51201 AN: 151886 Hom.: 8948 Cov.: 33 AF XY: 0.340 AC XY: 25197 AN XY: 74200

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.337

Alfa AF: 0.358 Hom.: 13268

Bravo AF: 0.330

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.4
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7828042; hg19: chr8-143819383;