rs4298845

chr10-83139600-G-C

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 0.791 in 152,120 control chromosomes in the GnomAD database, including 47,845 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 0.79 (47845 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.815 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: 0.791 AC: 120265 AN: 152002 Hom.: 47799 Cov.: 33

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.903

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.791 AC: 120366 AN: 152120 Hom.: 47845 Cov.: 33 AF XY: 0.788 AC XY: 58557 AN XY: 74340

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.821

Gnomad4 OTH AF: 0.799

Alfa AF: 0.812 Hom.: 6254

Bravo AF: 0.791

Asia WGS AF: 0.665 AC: 2310 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.4
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4298845; hg19: chr10-84899356;