rs4298845

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
• Publications: 2 publications found

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

African (AFR) AF: 0.777 AC: 32258 AN: 41522

American (AMR) AF: 0.816 AC: 12449 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2736 AN: 3472

East Asian (EAS) AF: 0.541 AC: 2795 AN: 5164

South Asian (SAS) AF: 0.688 AC: 3318 AN: 4822

European-Finnish (FIN) AF: 0.780 AC: 8248 AN: 10580

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.821 AC: 55830 AN: 67996

Other (OTH) AF: 0.799 AC: 1688 AN: 2112

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4298845; hg19: chr10-84899356;