chr10-83139600-G-C

Variant names:

• chr10-83139600-G-C
• rs4298845

Variant summary

Our verdict is Benign. The variant received -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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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 AC: 0.776889 AN: 0.776889

Gnomad4 AMR AF: 0.816 AC: 0.816435 AN: 0.816435

Gnomad4 ASJ AF: 0.788 AC: 0.788018 AN: 0.788018

Gnomad4 EAS AF: 0.541 AC: 0.541247 AN: 0.541247

Gnomad4 SAS AF: 0.688 AC: 0.688096 AN: 0.688096

Gnomad4 FIN AF: 0.780 AC: 0.779584 AN: 0.779584

Gnomad4 NFE AF: 0.821 AC: 0.821078 AN: 0.821078

Gnomad4 OTH AF: 0.799 AC: 0.799242 AN: 0.799242

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;