rs3121323

Variant names:

• chr10-42881718-G-A
• rs3121323

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 0.135 in 152,130 control chromosomes in the GnomAD database, including 1,516 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 0.14 (1516 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 7 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 (SAS) allele frequency at 95% confidence interval = 0.162 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: 0.135 AC: 20545 AN: 152012 Hom.: 1516 Cov.: 33

Gnomad AFR AF: 0.0765

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.135 AC: 20553 AN: 152130 Hom.: 1516 Cov.: 33 AF XY: 0.135 AC XY: 10031 AN XY: 74368

African (AFR) AF: 0.0764 AC: 3174 AN: 41542

American (AMR) AF: 0.153 AC: 2344 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3470

East Asian (EAS) AF: 0.144 AC: 743 AN: 5174

South Asian (SAS) AF: 0.171 AC: 822 AN: 4804

European-Finnish (FIN) AF: 0.137 AC: 1457 AN: 10602

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11202 AN: 67934

Other (OTH) AF: 0.134 AC: 283 AN: 2114

Alfa AF: 0.145 Hom.: 2373

Bravo AF: 0.134

Asia WGS AF: 0.183 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.67
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs3121323; hg19: chr10-43377166;