3-145418990-C-A

Position:

• chr3-145418990-C-A

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 0.087 in 151,760 control chromosomes in the GnomAD database, including 741 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 0.087 (741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0871 AC: 13211 AN: 151644 Hom.: 743 Cov.: 32

Gnomad AFR AF: 0.0221

Gnomad AMI AF: 0.0299

Gnomad AMR AF: 0.0852

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0870 AC: 13203 AN: 151760 Hom.: 741 Cov.: 32 AF XY: 0.0862 AC XY: 6390 AN XY: 74168

Gnomad4 AFR AF: 0.0221

Gnomad4 AMR AF: 0.0852

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.0986

Gnomad4 FIN AF: 0.0817

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0955 Hom.: 133

Bravo AF: 0.0834

Asia WGS AF: 0.132 AC: 459 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.67
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs344985; hg19: chr3-145136777;