rs7840827

chr8-42112252-G-A

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 0.303 in 152,070 control chromosomes in the GnomAD database, including 9,288 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 0.30 (9288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 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: 0.303 AC: 45988 AN: 151952 Hom.: 9269 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.303 AC: 46047 AN: 152070 Hom.: 9288 Cov.: 32 AF XY: 0.300 AC XY: 22323 AN XY: 74346

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.0881

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.282

Alfa AF: 0.266 Hom.: 1602

Bravo AF: 0.302

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.1
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7840827; hg19: chr8-41969770;