rs10490787

chr3-42334864-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0292 in 152,124 control chromosomes in the GnomAD database, including 88 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 0.029 (88 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0292 (4447/152124) while in subpopulation NFE AF= 0.0422 (2869/67976). AF 95% confidence interval is 0.0409. There are 88 homozygotes in gnomad4. There are 2091 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 87 gene

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: 0.0293 AC: 4450 AN: 152006 Hom.: 87 Cov.: 33

Gnomad AFR AF: 0.00739

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0285

Gnomad ASJ AF: 0.0737

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0308

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0422

Gnomad OTH AF: 0.0488

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

GnomAD4 genome AF: 0.0292 AC: 4447 AN: 152124 Hom.: 88 Cov.: 33 AF XY: 0.0281 AC XY: 2091 AN XY: 74356

Gnomad4 AFR AF: 0.00737

Gnomad4 AMR AF: 0.0285

Gnomad4 ASJ AF: 0.0737

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0241

Gnomad4 FIN AF: 0.0308

Gnomad4 NFE AF: 0.0422

Gnomad4 OTH AF: 0.0483

Alfa AF: 0.0354 Hom.: 13

Bravo AF: 0.0288

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.0
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490787; hg19: chr3-42376356;