3-186867738-C-T

Variant names:

• chr3-186867738-C-T
• rs17373414

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 0.0716 in 152,246 control chromosomes in the GnomAD database, including 560 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 0.072 (560 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 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: 0.0717 AC: 10904 AN: 152128 Hom.: 561 Cov.: 32

Gnomad AFR AF: 0.0192

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0627

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0391

Gnomad FIN AF: 0.0343

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0807

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

GnomAD4 genome AF: 0.0716 AC: 10901 AN: 152246 Hom.: 560 Cov.: 32 AF XY: 0.0670 AC XY: 4989 AN XY: 74432

Gnomad4 AFR AF: 0.0191

Gnomad4 AMR AF: 0.0626

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0396

Gnomad4 FIN AF: 0.0343

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0799

Alfa AF: 0.0734 Hom.: 156

Bravo AF: 0.0720

Asia WGS AF: 0.0180 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17373414; hg19: chr3-186585527;