3-145456001-A-G

Variant names:

• chr3-145456001-A-G
• rs345013

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 0.099 in 152,186 control chromosomes in the GnomAD database, including 823 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 0.099 (823 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

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 (EAS) allele frequency at 95% confidence interval = 0.141 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: 0.0991 AC: 15069 AN: 152068 Hom.: 825 Cov.: 32

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0822

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.0990 AC: 15062 AN: 152186 Hom.: 823 Cov.: 32 AF XY: 0.0973 AC XY: 7239 AN XY: 74412

Gnomad4 AFR AF: 0.0621

Gnomad4 AMR AF: 0.0908

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0822

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.112

Alfa AF: 0.117 Hom.: 1085

Bravo AF: 0.0975

Asia WGS AF: 0.136 AC: 471 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.61
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs345013; hg19: chr3-145173788; COSMIC: COSV50192802;