3-164872151-C-T

Position:

• chr3-164872151-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 0.232 in 152,044 control chromosomes in the GnomAD database, including 7,407 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 0.23 (7407 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.164872151C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35191 AN: 151926 Hom.: 7384 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0909

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.232 AC: 35251 AN: 152044 Hom.: 7407 Cov.: 32 AF XY: 0.224 AC XY: 16617 AN XY: 74322

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0909

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0520

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.182

Alfa AF: 0.176 Hom.: 605

Bravo AF: 0.252

Asia WGS AF: 0.127 AC: 440 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2168784; hg19: chr3-164589939;