rs848413

Variant names:

• chr7-108870756-C-G
• rs848413

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 0.157 in 144,112 control chromosomes in the GnomAD database, including 5,780 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 0.16 (5780 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 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: 0.156 AC: 22509 AN: 144056 Hom.: 5761 Cov.: 29

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0601

Gnomad ASJ AF: 0.0370

Gnomad EAS AF: 0.000204

Gnomad SAS AF: 0.00177

Gnomad FIN AF: 0.000227

Gnomad MID AF: 0.0552

Gnomad NFE AF: 0.00293

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.157 AC: 22564 AN: 144112 Hom.: 5780 Cov.: 29 AF XY: 0.152 AC XY: 10579 AN XY: 69738

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.0599

Gnomad4 ASJ AF: 0.0370

Gnomad4 EAS AF: 0.000205

Gnomad4 SAS AF: 0.00155

Gnomad4 FIN AF: 0.000227

Gnomad4 NFE AF: 0.00293

Gnomad4 OTH AF: 0.121

Alfa AF: 0.105 Hom.: 436

Bravo AF: 0.180

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs848413; hg19: chr7-108510813;