3-166243323-A-G

Variant names:

• chr3-166243323-A-G
• rs1371901

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 0.688 in 151,852 control chromosomes in the GnomAD database, including 36,083 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 0.69 (36083 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.761 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: 0.688 AC: 104427 AN: 151732 Hom.: 36055 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.688 AC: 104517 AN: 151852 Hom.: 36083 Cov.: 31 AF XY: 0.696 AC XY: 51621 AN XY: 74196

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.665

Alfa AF: 0.683 Hom.: 73070

Bravo AF: 0.673

Asia WGS AF: 0.737 AC: 2562 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.54
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1371901; hg19: chr3-165961111;