3-166347311-T-C

Position:

• chr3-166347311-T-C

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 0.289 in 152,024 control chromosomes in the GnomAD database, including 7,888 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 0.29 (7888 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.166347311T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43927 AN: 151908 Hom.: 7891 Cov.: 32

Gnomad AFR AF: 0.0866

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.289 AC: 43923 AN: 152024 Hom.: 7888 Cov.: 32 AF XY: 0.294 AC XY: 21879 AN XY: 74306

Gnomad4 AFR AF: 0.0863

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.265

Alfa AF: 0.348 Hom.: 14005

Bravo AF: 0.268

Asia WGS AF: 0.482 AC: 1674 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	6.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2863381; hg19: chr3-166065099;