3-1669864-C-T

Position:

• chr3-1669864-C-T

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 0.151 in 152,124 control chromosomes in the GnomAD database, including 2,259 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 0.15 (2259 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.1669864C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22886 AN: 152006 Hom.: 2246 Cov.: 32

Gnomad AFR AF: 0.0437

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.0871

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.151 AC: 22914 AN: 152124 Hom.: 2259 Cov.: 32 AF XY: 0.156 AC XY: 11625 AN XY: 74360

Gnomad4 AFR AF: 0.0438

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.0871

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.143

Alfa AF: 0.138 Hom.: 438

Bravo AF: 0.145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.021
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3856831; hg19: chr3-1711548;